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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2msdGNPMHC class I alpha chain

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2msdGNPMHC class I alpha chain/1.000
2mseGNPMHC class I alpha chain/0.563
2rgeGNPGTPase HRas/0.494
3pitGNPRas-related protein M-Ras/0.490
3bbpGTPRas-related protein Rab-6A/0.475
1xtrGNPGTP-binding protein Rheb/0.472
2dhfDZFDihydrofolate reductase1.5.1.30.472
3a6pGTPGTP-binding nuclear protein Ran/0.472
4dsnGCPGTPase KRas/0.472
4xo7NAPAldo-keto reductase family 1 member C2/0.472
4jtqNAPAldo-keto reductase family 1 member C2/0.471
2rgcGNPGTPase HRas/0.469
1diuBDMDihydrofolate reductase1.5.1.30.468
3ddcGNPGTPase HRas/0.468
1yhnGTPRas-related protein Rab-7a/0.467
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.464
2mscGDPMHC class I alpha chain/0.460
2rgbGNPGTPase HRas/0.459
3tgpGNPGTPase HRas/0.459
1disBDMDihydrofolate reductase1.5.1.30.458
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1m7bGTPRho-related GTP-binding protein RhoE/0.458
2cntCOARibosomal-protein-alanine acetyltransferase/0.458
4nv14TGFormyl transferase/0.458
3nxxNDPDihydrofolate reductase1.5.1.30.457
3ekuCY9Actin-5C/0.455
3kkoGNPRas-related protein M-Ras/0.454
3oesGNPGTPase RhebL1/0.454
1kmqGNPTransforming protein RhoA/0.452
3oivGNPGTPase HRas/0.452
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.452
1zc4GNPRas-related protein Ral-A/0.451
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
3oiwGNPGTPase HRas/0.451
3rs7GNPGTPase HRas/0.451
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.451
1xtsGTPGTP-binding protein Rheb/0.450
4nyjGNPGTPase HRas/0.449
3clbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.448
3bgiSAHThiopurine S-methyltransferase2.1.1.670.447
4g0nGNPGTPase HRas/0.447
4nyiGNPGTPase HRas/0.447
2fe4GDPRas-related protein Rab-6B/0.446
3i3sGNPGTPase HRas/0.446
3oiuGNPGTPase HRas/0.446
2gjnFMNNitronate monooxygenase1.13.12.160.445
2w3bNDPDihydrofolate reductase1.5.1.30.445
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.444
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.444
1dr2TAPDihydrofolate reductase1.5.1.30.443
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.443
4g95OAGDihydrofolate reductase1.5.1.30.442
3v4fGNPGTPase HRas/0.441
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.440
2gv8NDPThiol-specific monooxygenase1.14.130.440
2vbpVB1Isopenicillin N synthase1.21.3.10.440
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.440
3qemQEMGlutamate receptor ionotropic, NMDA 2B/0.440
3qemQEMNMDA glutamate receptor subunit/0.440
5esoISC2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.440