RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Goodsell, David S.; Zardecki, Christine; Di Costanzo, Luigi; Duarte, Jose M.; Hudson, Brian P.; Persikova, Irina; Segura, Joan; Shao, Chenghua; Voigt, Maria; Westbrook, John D.; Young, Jasmine Y.; Burley, Stephen K.

doi:10.1002/pro.3730

Title: RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Journal Article · Wed Sep 18 00:00:00 EDT 2019 · Protein Science

DOI:https://doi.org/10.1002/pro.3730· OSTI ID:1803879

^[1];

^[2]; Di Costanzo, Luigi ^[3];

^[4]; Hudson, Brian P. ^[2]; Persikova, Irina ^[2]; Segura, Joan ^[4]; Shao, Chenghua ^[2]; Voigt, Maria ^[2];

^[2];

^[5]

State University of New Jersey, Piscataway, NJ (United States); Rutgers Univ., Piscataway, NJ (United States); The Scripps Research Inst., La Jolla, CA (United States)
State University of New Jersey, Piscataway, NJ (United States); Rutgers Univ., Piscataway, NJ (United States)
State University of New Jersey, Piscataway, NJ (United States); Rutgers Univ., Piscataway, NJ (United States); Univ. of Naples Federico II (Italy)
Univ. of California, San Diego, CA (United States)
State University of New Jersey, Piscataway, NJ (United States); Rutgers Univ., Piscataway, NJ (United States); Univ. of California, San Diego, CA (United States); State University of New Jersey, New Brunswick, NJ (United States

Abstract Analyses of publicly available structural data reveal interesting insights into the impact of the three‐dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G‐protein‐coupled receptors, voltage‐gated ion channels, ligand‐gated ion channels, transporters, and E3 ubiquitin ligases). The Protein Data Bank (PDB) archive currently holds > 155,000 atomic‐level 3D structures of biomolecules experimentally determined using crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy. The PDB was established in 1971 as the first open‐access, digital‐data resource in biology, and is now managed by the Worldwide PDB partnership (wwPDB; wwPDB.org ). US PDB operations are the responsibility of the Research Collaboratory for Structural Bioinformatics PDB (RCSB PDB). The RCSB PDB serves millions of RCSB.org users worldwide by delivering PDB data integrated with ∼40 external biodata resources, providing rich structural views of fundamental biology, biomedicine, and energy sciences. Recently published work showed that the PDB archival holdings facilitated discovery of ∼90% of the 210 new drugs approved by the US Food and Drug Administration 2010–2016. We review user‐driven development of RCSB PDB services, examine growth of the PDB archive in terms of size and complexity, and present examples and opportunities for structure‐guided drug discovery for challenging targets (e.g., integral membrane proteins).

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

Research Organization:: Rutgers Univ., Piscataway, NJ (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: SC0019749; DBI-1832184; R01GM133198; DE‐SC0019749

OSTI ID:: 1803879

Alternate ID(s):: OSTI ID: 1576653

Journal Information:: Protein Science, Vol. 29, Issue 1; ISSN 0961-8368

Publisher:: The Protein SocietyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 164 works

Citation information provided by
Web of Science

References (107)

The G-Protein-Coupled Receptors in the Human Genome Form Five Main Families. Phylogenetic Analysis, Paralogon Groups, and Fingerprints Fredriksson, Robert; Lagerström, Malin C.; Lundin, Lars-Gustav Molecular Pharmacology, Vol. 63, Issue 6 https://doi.org/10.1124/mol.63.6.1256	journal	June 2003
X-ray structure of a voltage-dependent K+ channel Jiang, Youxing; Lee, Alice; Chen, Jiayun Nature, Vol. 423, Issue 6935 https://doi.org/10.1038/nature01580	journal	May 2003
The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology Goodsell, David S.; Dutta, Shuchismita; Zardecki, Christine PLOS Biology, Vol. 13, Issue 5 https://doi.org/10.1371/journal.pbio.1002140	journal	May 2015
NGL viewer: web-based molecular graphics for large complexes Rose, Alexander S.; Bradley, Anthony R.; Valasatava, Yana Bioinformatics, Vol. 34, Issue 21 https://doi.org/10.1093/bioinformatics/bty419	journal	May 2018
New design strategies for antidepressant drugs Immadisetty, Kalyan; Geffert, Laura M.; Surratt, Christopher K. Expert Opinion on Drug Discovery, Vol. 8, Issue 11 https://doi.org/10.1517/17460441.2013.830102	journal	August 2013
Economic Impacts of the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank Sullivan, Kevin P.; Brennan-Tonetta, Peggy; Marxen, Lucas J. RCSB Protein Data Bank https://doi.org/10.2210/rcsb_pdb/pdb-econ-imp-2017	journal	May 2017
The Resolution Revolution Kuhlbrandt, W. Science, Vol. 343, Issue 6178 https://doi.org/10.1126/science.1251652	journal	March 2014
Structural Models of Ligand-Gated Ion Channels: Sites of Action for Anesthetics and Ethanol Olsen, Richard W.; Li, Guo-Dong; Wallner, Martin Alcoholism: Clinical and Experimental Research, Vol. 38, Issue 3 https://doi.org/10.1111/acer.12283	journal	October 2013
Structures of human Na _v 1.7 channel in complex with auxiliary subunits and animal toxins Shen, Huaizong; Liu, Dongliang; Wu, Kun Science, Vol. 363, Issue 6433 https://doi.org/10.1126/science.aaw2493	journal	February 2019
RCSB Protein Data Bank: Sustaining A Living Digital Data Resource That Enables Breakthroughs In Scientific Research And Biomedical Education Burley, Stephen K.; Berman, Helen M.; Christie, Cole The FASEB Journal, Vol. 32, Issue S1 https://doi.org/10.1096/fasebj.2018.32.1_supplement.674.3	journal	April 2018
GLP-1 as a target for therapeutic intervention Rajeev, Surya Panicker; Wilding, John Current Opinion in Pharmacology, Vol. 31 https://doi.org/10.1016/j.coph.2016.08.005	journal	December 2016
Structure of the human voltage-gated sodium channel Na _v 1.4 in complex with β1 Pan, Xiaojing; Li, Zhangqiang; Zhou, Qiang Science, Vol. 362, Issue 6412 https://doi.org/10.1126/science.aau2486	journal	September 2018
Plant ubiquitin ligases as signaling hubs Shabek, Nitzan; Zheng, Ning Nature Structural & Molecular Biology, Vol. 21, Issue 4 https://doi.org/10.1038/nsmb.2804	journal	April 2014
Protacs: Chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation Sakamoto, K. M.; Kim, K. B.; Kumagai, A. Proceedings of the National Academy of Sciences, Vol. 98, Issue 15 https://doi.org/10.1073/pnas.141230798	journal	July 2001
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education: RCSB Protein Data Bank Burley, Stephen K.; Berman, Helen M.; Christie, Cole Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3331	journal	November 2017
Structure and mechanism of AMPA receptor — auxiliary protein complexes Chen, Shanshuang; Gouaux, Eric Current Opinion in Structural Biology, Vol. 54 https://doi.org/10.1016/j.sbi.2019.01.011	journal	February 2019
Classics in Chemical Neuroscience: Memantine Alam, Shahrina; Lingenfelter, Kaelyn Skye; Bender, Aaron M. ACS Chemical Neuroscience, Vol. 8, Issue 9 https://doi.org/10.1021/acschemneuro.7b00270	journal	July 2017
Modulation of Ligand-gated Ion Channels by Antidepressants and Antipsychotics Rammes, Gerhard; Rupprecht, Rainer Molecular Neurobiology, Vol. 35, Issue 2 https://doi.org/10.1007/s12035-007-0006-1	journal	September 2007
The ABCs of membrane transporters in health and disease (SLC series): Introduction Hediger, Matthias A.; Clémençon, Benjamin; Burrier, Robert E. Molecular Aspects of Medicine, Vol. 34, Issue 2-3 https://doi.org/10.1016/j.mam.2012.12.009	journal	April 2013
Adhesion G Protein-Coupled Receptors as Drug Targets for Neurological Diseases Folts, Christopher J.; Giera, Stefanie; Li, Tao Trends in Pharmacological Sciences, Vol. 40, Issue 4 https://doi.org/10.1016/j.tips.2019.02.003	journal	April 2019
Overview of Transporters in Pharmacokinetics and Drug Discovery Zhang, Yan Current Protocols in Pharmacology, Vol. 82, Issue 1 https://doi.org/10.1002/cpph.46	journal	August 2018
The VGL-Chanome: A Protein Superfamily Specialized for Electrical Signaling and Ionic Homeostasis Yu, F. H.; Catterall, W. A. Science Signaling, Vol. 2004, Issue 253 https://doi.org/10.1126/stke.2532004re15	journal	September 2004
Structure of a Conjugating Enzyme-Ubiquitin Thiolester Intermediate Reveals a Novel Role for the Ubiquitin Tail Hamilton, Katherine S.; Ellison, Michael J.; Barber, Kathryn R. Structure, Vol. 9, Issue 10 https://doi.org/10.1016/S0969-2126(01)00657-8	journal	October 2001
GPCR Engineering Yields High-Resolution Structural Insights into 2-Adrenergic Receptor Function Rosenbaum, D. M.; Cherezov, V.; Hanson, M. A. Science, Vol. 318, Issue 5854 https://doi.org/10.1126/science.1150609	journal	October 2007
Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM Roh, Soung-Hun; Hryc, Corey F.; Jeong, Hyun-Hwan Proceedings of the National Academy of Sciences, Vol. 114, Issue 31 https://doi.org/10.1073/pnas.1704725114	journal	July 2017
Analysis of impact metrics for the Protein Data Bank Markosian, Christopher; Di Costanzo, Luigi; Sekharan, Monica Scientific Data, Vol. 5, Issue 1 https://doi.org/10.1038/sdata.2018.212	journal	October 2018
A CFTR Potentiator in Patients with Cystic Fibrosis and the G551D Mutation Ramsey, Bonnie W.; Davies, Jane; McElvaney, N. Gerard New England Journal of Medicine, Vol. 365, Issue 18 https://doi.org/10.1056/NEJMoa1105185	journal	November 2011
Crystallizing membrane proteins using lipidic mesophases Caffrey, Martin; Cherezov, Vadim Nature Protocols, Vol. 4, Issue 5 https://doi.org/10.1038/nprot.2009.31	journal	April 2009
Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation Lü, Wei; Du, Juan; Goehring, April Science, Vol. 355, Issue 6331 https://doi.org/10.1126/science.aal3729	journal	February 2017
Glutamate Receptor Ion Channels: Structure, Regulation, and Function Traynelis, Stephen F.; Wollmuth, Lonnie P.; McBain, Chris J. Pharmacological Reviews, Vol. 62, Issue 3 https://doi.org/10.1124/pr.109.002451	journal	August 2010
Structural basis for the mechanism of ABC transporters Beis, Konstantinos Biochemical Society Transactions, Vol. 43, Issue 5 https://doi.org/10.1042/BST20150047	journal	October 2015
Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex Zheng, Ning; Schulman, Brenda A.; Song, Langzhou Nature, Vol. 416, Issue 6882 https://doi.org/10.1038/416703a	journal	April 2002
An outlook on using serial femtosecond crystallography in drug discovery Mishin, Alexey; Gusach, Anastasiia; Luginina, Aleksandra Expert Opinion on Drug Discovery, Vol. 14, Issue 9 https://doi.org/10.1080/17460441.2019.1626822	journal	May 2019
Hepatitis E vaccine debuts Park, Soo Bin Nature, Vol. 491, Issue 7422 https://doi.org/10.1038/491021a	journal	October 2012
The emerging complexity of protein ubiquitination Komander, David Biochemical Society Transactions, Vol. 37, Issue 5 https://doi.org/10.1042/BST0370937	journal	September 2009
Voltage-gated sodium channels: structures, functions, and molecular modeling Xu, Lei; Ding, Xiaoqin; Wang, Tianhu Drug Discovery Today, Vol. 24, Issue 7 https://doi.org/10.1016/j.drudis.2019.05.014	journal	July 2019
UniProt: the universal protein knowledgebase UniProt Consortium, The Nucleic Acids Research, Vol. 46, Issue 5 https://doi.org/10.1093/nar/gky092	journal	February 2018
Separation of two different populations of axial organ cells of Asterias rubens by the use of lectins Redziniak, Gérard; Leclerc, Michel; Panijel, Jacques Biochimie, Vol. 60, Issue 5 https://doi.org/10.1016/S0300-9084(78)80869-4	journal	September 1978
Crystal Structure of the Ligand-bound Glucagon-like Peptide-1 Receptor Extracellular Domain Runge, Steffen; Thøgersen, Henning; Madsen, Kjeld Journal of Biological Chemistry, Vol. 283, Issue 17 https://doi.org/10.1074/jbc.M708740200	journal	February 2008
Utility of protein structures in overcoming ADMET-related issues of drug-like compounds Stoll, Friederike; Göller, Andreas H.; Hillisch, Alexander Drug Discovery Today, Vol. 16, Issue 11-12 https://doi.org/10.1016/j.drudis.2011.04.008	journal	June 2011
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj): New tools and functions in PDBj data-out Kinjo, Akira R.; Bekker, Gert-Jan; Wako, Hiroshi Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3273	journal	September 2017
Plasticity in binding confers selectivity in ligand-induced protein degradation Nowak, Radosław P.; DeAngelo, Stephen L.; Buckley, Dennis Nature Chemical Biology, Vol. 14, Issue 7 https://doi.org/10.1038/s41589-018-0055-y	journal	June 2018
The Transporter Classification Database (TCDB): recent advances Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1103	journal	November 2015
The Pfam protein families database: towards a more sustainable future Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1344	journal	December 2015
Structure and Mechanism of the Lactose Permease of Escherichia coli Abramson, J. Science, Vol. 301, Issue 5633 https://doi.org/10.1126/science.1088196	journal	August 2003
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor Palczewski, K. Science, Vol. 289, Issue 5480 https://doi.org/10.1126/science.289.5480.739	journal	August 2000
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1004	journal	October 2018
Structure of P-Glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding Aller, S. G.; Yu, J.; Ward, A. Science, Vol. 323, Issue 5922 https://doi.org/10.1126/science.1168750	journal	March 2009
Allosteric Modulation of Ionotropic Glutamate Receptors Special Issue Carruthers, Nicholas I.; Lovenberg, Timothy W.; Traynelis, Stephen F. ACS Medicinal Chemistry Letters, Vol. 10, Issue 3 https://doi.org/10.1021/acsmedchemlett.9b00047	journal	November 2018
X-ray structures and mechanism of the human serotonin transporter Coleman, Jonathan A.; Green, Evan M.; Gouaux, Eric Nature, Vol. 532, Issue 7599 https://doi.org/10.1038/nature17629	journal	April 2016
Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma Bollag, Gideon; Hirth, Peter; Tsai, James Nature, Vol. 467, Issue 7315 https://doi.org/10.1038/nature09454	journal	September 2010
The E. coli BtuCD Structure: A Framework for ABC Transporter Architecture and Mechanism Locher, K. P. Science, Vol. 296, Issue 5570 https://doi.org/10.1126/science.1071142	journal	May 2002
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource Velankar, Sameer; Dana, José M.; Jacobsen, Julius Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1258	journal	November 2012
A complicated complex: Ion channels, voltage sensing, cell membranes and peptide inhibitors Zhang, Alan H.; Sharma, Gagan; Undheim, Eivind A. B. Neuroscience Letters, Vol. 679 https://doi.org/10.1016/j.neulet.2018.04.030	journal	July 2018
An SCN9A channelopathy causes congenital inability to experience pain Cox, James J.; Reimann, Frank; Nicholas, Adeline K. Nature, Vol. 444, Issue 7121 https://doi.org/10.1038/nature05413	journal	December 2006
Cryo-EM structure of the activated GLP-1 receptor in complex with a G protein Zhang, Yan; Sun, Bingfa; Feng, Dan Nature, Vol. 546, Issue 7657 https://doi.org/10.1038/nature22394	journal	May 2017
Cystic fibrosis Elborn, J. Stuart The Lancet, Vol. 388, Issue 10059 https://doi.org/10.1016/S0140-6736(16)00576-6	journal	November 2016
A primer on the mechanics of P-glycoprotein the multidrug transporter Hennessy, M.; Spiers, J. P. Pharmacological Research, Vol. 55, Issue 1 https://doi.org/10.1016/j.phrs.2006.10.007	journal	January 2007
SWISS-MODEL: homology modelling of protein structures and complexes Waterhouse, Andrew; Bertoni, Martino; Bienert, Stefan Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky427	journal	May 2018
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Protein Data Bank: the single global archive for 3D macromolecular structure data Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky949	journal	October 2018
Structural identification of a hotspot on CFTR for potentiation Liu, Fangyu; Zhang, Zhe; Levit, Anat Science, Vol. 364, Issue 6446 https://doi.org/10.1126/science.aaw7611	journal	June 2019
Ivermectin: uses and impact 20 years on Fox, LeAnne M. Current Opinion in Infectious Diseases, Vol. 19, Issue 6 https://doi.org/10.1097/QCO.0b013e328010774c	journal	January 2006
Molecular mechanisms of cereblon-based drugs Asatsuma-Okumura, Tomoko; Ito, Takumi; Handa, Hiroshi Pharmacology & Therapeutics, Vol. 202 https://doi.org/10.1016/j.pharmthera.2019.06.004	journal	October 2019
Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification Zhang, Cheng; Cantara, William; Jeon, Youngmin Ultramicroscopy, Vol. 203 https://doi.org/10.1016/j.ultramic.2018.11.016	journal	August 2019
Impact Analysis of "Berman HM et al., (2000), The Protein Data Bank" Basner, Jodi RCSB Protein Data Bank https://doi.org/10.2210/rcsb_pdb/pdb-cit-anal-2017	journal	May 2017
UniProt: the universal protein knowledgebase Nucleic Acids Research, Vol. 45, Issue D1, p. D158-D169 https://doi.org/10.1093/nar/gkw1099	journal	November 2016
Structural biology of solute carrier (SLC) membrane transport proteins Bai, Xiaoyun; Moraes, Trevor F.; Reithmeier, Reinhart A. F. Molecular Membrane Biology, Vol. 34, Issue 1-2 https://doi.org/10.1080/09687688.2018.1448123	journal	February 2017
Ubiquitin Ligases: Structure, Function, and Regulation Zheng, Ning; Shabek, Nitzan Annual Review of Biochemistry, Vol. 86, Issue 1 https://doi.org/10.1146/annurev-biochem-060815-014922	journal	June 2017
Structure and mechanism of ABC transporters Wilkens, Stephan F1000Prime Reports, Vol. 7 https://doi.org/10.12703/P7-14	journal	February 2015
The Structure of the APPBP1-UBA3-NEDD8-ATP Complex Reveals the Basis for Selective Ubiquitin-like Protein Activation by an E1 Walden, Helen; Podgorski, Michael S.; Huang, Danny T. Molecular Cell, Vol. 12, Issue 6 https://doi.org/10.1016/S1097-2765(03)00452-0	journal	December 2003
Potentiating SLC transporter activity: Emerging drug discovery opportunities Rives, Marie-Laure; Javitch, Jonathan A.; Wickenden, Alan D. Biochemical Pharmacology, Vol. 135 https://doi.org/10.1016/j.bcp.2017.02.010	journal	July 2017
X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor Sobolevsky, Alexander I.; Rosconi, Michael P.; Gouaux, Eric Nature, Vol. 462, Issue 7274 https://doi.org/10.1038/nature08624	journal	November 2009
Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography Olmos, Jose L.; Pandey, Suraj; Martin-Garcia, Jose M. BMC Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s12915-018-0524-5	journal	May 2018
Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters Yamashita, Atsuko; Singh, Satinder K.; Kawate, Toshimitsu Nature, Vol. 437, Issue 7056 https://doi.org/10.1038/nature03978	journal	July 2005
Insights into SCF ubiquitin ligases from the structure of the Skp1–Skp2 complex Schulman, Brenda A.; Carrano, Andrea C.; Jeffrey, Philip D. Nature, Vol. 408, Issue 6810 https://doi.org/10.1038/35042620	journal	November 2000
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank Westbrook, John D.; Shao, Chenghua; Feng, Zukang Bioinformatics, Vol. 31, Issue 8 https://doi.org/10.1093/bioinformatics/btu789	journal	December 2014
Glutamate receptors at atomic resolution Mayer, Mark L. Nature, Vol. 440, Issue 7083 https://doi.org/10.1038/nature04709	journal	March 2006
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals Westbrook, John D.; Burley, Stephen K. Structure, Vol. 27, Issue 2 https://doi.org/10.1016/j.str.2018.11.007	journal	February 2019
The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity Doyle, D. A. Science, Vol. 280, Issue 5360 https://doi.org/10.1126/science.280.5360.69	journal	April 1998
Targeting Cullin–RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation Bulatov, Emil; Ciulli, Alessio Biochemical Journal, Vol. 467, Issue 3 https://doi.org/10.1042/BJ20141450	journal	April 2015
Refined Structure of the Nicotinic Acetylcholine Receptor at 4Å Resolution Unwin, Nigel Journal of Molecular Biology, Vol. 346, Issue 4 https://doi.org/10.1016/j.jmb.2004.12.031	journal	March 2005
Structure-Function of the G Protein–Coupled Receptor Superfamily Katritch, Vsevolod; Cherezov, Vadim; Stevens, Raymond C. Annual Review of Pharmacology and Toxicology, Vol. 53, Issue 1 https://doi.org/10.1146/annurev-pharmtox-032112-135923	journal	January 2013
A Call for Systematic Research on Solute Carriers César-Razquin, Adrián; Snijder, Berend; Frappier-Brinton, Tristan Cell, Vol. 162, Issue 3 https://doi.org/10.1016/j.cell.2015.07.022	journal	July 2015
From Toxins Targeting Ligand Gated Ion Channels to Therapeutic Molecules Nasiripourdori, Adak; Taly, Valérie; Grutter, Thomas Toxins, Vol. 3, Issue 3 https://doi.org/10.3390/toxins3030260	journal	March 2011
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank Gao, Jianjiong; Prlić, Andreas; Bi, Chunxiao Bioinformatics, Vol. 33, Issue 13 https://doi.org/10.1093/bioinformatics/btx101	journal	February 2017
Dissecting diverse functions of NMDA receptors by structural biology Wang, Jue Xiang; Furukawa, Hiro Current Opinion in Structural Biology, Vol. 54 https://doi.org/10.1016/j.sbi.2018.12.009	journal	February 2019
Crystal Structure of the Maltose Transporter in a Pretranslocation Intermediate State Oldham, M. L.; Chen, J. Science, Vol. 332, Issue 6034 https://doi.org/10.1126/science.1200767	journal	May 2011
The crystal structure of a voltage-gated sodium channel Payandeh, Jian; Scheuer, Todd; Zheng, Ning Nature, Vol. 475, Issue 7356 https://doi.org/10.1038/nature10238	journal	July 2011
Molecular basis for pore blockade of human Na ⁺ channel Na _v 1.2 by the μ-conotoxin KIIIA Pan, Xiaojing; Li, Zhangqiang; Huang, Xiaoshuang Science, Vol. 363, Issue 6433 https://doi.org/10.1126/science.aaw2999	journal	February 2019
Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor Crystallogenesis Thorsen, Thor Seneca; Matt, Rachel; Weis, William I. Structure, Vol. 22, Issue 11 https://doi.org/10.1016/j.str.2014.08.022	journal	November 2014
Alternating Access in Maltose Transporter Mediated by Rigid-Body Rotations Khare, Dheeraj; Oldham, Michael L.; Orelle, Cedric Molecular Cell, Vol. 33, Issue 4 https://doi.org/10.1016/j.molcel.2009.01.035	journal	February 2009
Crystal structure of a catalytic intermediate of the maltose transporter Oldham, Michael L.; Khare, Dheeraj; Quiocho, Florante A. Nature, Vol. 450, Issue 7169 https://doi.org/10.1038/nature06264	journal	November 2007
Crystallography: Protein Data Bank Skipper, Magdalena Nature New Biology, Vol. 233, Issue 42, p. 223-223 https://doi.org/10.1038/newbio233223b0	journal	October 1971
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe Mir, Saqib; Alhroub, Younes; Anyango, Stephen Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1070	journal	November 2017
BioMagResBank Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm957	journal	December 2007
A comprehensive map of molecular drug targets Santos, Rita; Ursu, Oleg; Gaulton, Anna Nature Reviews Drug Discovery, Vol. 16, Issue 1 https://doi.org/10.1038/nrd.2016.230	journal	December 2016
Gene Ontology Consortium: going forward Consortium, Gene Ontology Nucleic Acids Research, Vol. 43, Issue D1, p. D1049-D1056 https://doi.org/10.1093/nar/gku1179	journal	January 2014
Adhesion G Protein–Coupled Receptors as Drug Targets Purcell, Ryan H.; Hall, Randy A. Annual Review of Pharmacology and Toxicology, Vol. 58, Issue 1 https://doi.org/10.1146/annurev-pharmtox-010617-052933	journal	January 2018
A nomenclature for ligand-gated ion channels Collingridge, Graham L.; Olsen, Richard W.; Peters, John Neuropharmacology, Vol. 56, Issue 1 https://doi.org/10.1016/j.neuropharm.2008.06.063	journal	January 2009
Voltage gated sodium channels as drug discovery targets Bagal, Sharan K.; Marron, Brian E.; Owen, Robert M. Channels, Vol. 9, Issue 6 https://doi.org/10.1080/19336950.2015.1079674	journal	July 2015
Functional Insights from Glutamate Receptor Ion Channel Structures Kumar, Janesh; Mayer, Mark L. Annual Review of Physiology, Vol. 75, Issue 1 https://doi.org/10.1146/annurev-physiol-030212-183711	journal	February 2013
Voltage-Gated Sodium Channels: Structure, Function, Pharmacology, and Clinical Indications de Lera Ruiz, Manuel; Kraus, Richard L. Journal of Medicinal Chemistry, Vol. 58, Issue 18 https://doi.org/10.1021/jm501981g	journal	May 2015
ModBase, a database of annotated comparative protein structure models and associated resources Pieper, Ursula; Webb, Benjamin M.; Dong, Guang Qiang Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1144	journal	November 2013
Structural basis of PROTAC cooperative recognition for selective protein degradation Gadd, Morgan S.; Testa, Andrea; Lucas, Xavier Nature Chemical Biology, Vol. 13, Issue 5 https://doi.org/10.1038/nchembio.2329	journal	March 2017
Discovery of the Once-Weekly Glucagon-Like Peptide-1 (GLP-1) Analogue Semaglutide Lau, Jesper; Bloch, Paw; Schäffer, Lauge Journal of Medicinal Chemistry, Vol. 58, Issue 18 https://doi.org/10.1021/acs.jmedchem.5b00726	journal	September 2015
Mutations in SCN9A, encoding a sodium channel alpha subunit, in patients with primary erythermalgia Yang, Y. Journal of Medical Genetics, Vol. 41, Issue 3 https://doi.org/10.1136/jmg.2003.012153	journal	March 2004

Cited By (2)

The Masked Polar Group Incorporation (MPGI) Strategy in Drug Design: Effects of Nitrogen Substitutions on Combretastatin and Isocombretastatin Tubulin Inhibitors Molecules, Vol. 24, Issue 23 https://doi.org/10.3390/molecules24234319	journal	November 2019
Investigating the multi-target pharmacological mechanism of danhong injection acting on unstable angina by combined network pharmacology and molecular docking Guo, Siyu; Wu, Jiarui; Zhou, Wei BMC Complementary Medicine and Therapies, Vol. 20, Issue 1 https://doi.org/10.1186/s12906-020-2853-5	journal	March 2020

Similar Records

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Journal Article · Fri Oct 22 00:00:00 EDT 2021 · Protein Science · OSTI ID:1803879

Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao; +32 more

PDB Structure Data Impacted Discovery and Development of Recently FDA‐Approved Drugs

Journal Article · Mon Apr 01 00:00:00 EDT 2019 · FASEB Journal · OSTI ID:1803879

Zardecki, Christine; Westbrook, John; Burley, Stephen K.

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Journal Article · Wed Nov 16 00:00:00 EST 2022 · Protein Science · OSTI ID:1803879

Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao; +38 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
biochemistry & molecular biology
protein structure and function
structural biology
Protein Data Bank
PDB
structure-guided drug discovery
integral membrane proteins
GPCR
ion channel
transporter
ubiquitin ligase

Title: RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Citation Formats

References (107)

Cited By (2)

Similar Records

Related Subjects