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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
4l8gGDPGTPase KRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4l8gGDPGTPase KRas/1.000
4l9sGDPGTPase HRas/0.684
2rggGNPGTPase HRas/0.647
4lpkGDPGTPase KRas/0.641
4q02GDPGTPase KRas/0.640
4lv6GDPGTPase KRas/0.633
4tq9GDPGTPase KRas/0.629
4lrwGDPGTPase KRas/0.628
4xvqGNPGTPase HRas/0.626
4epwGDPGTPase KRas/0.622
4epxGDPGTPase KRas/0.622
4wa7GDPGTPase KRas/0.621
2ce2GDPGTPase HRas/0.619
4q03GDPGTPase KRas/0.614
4obeGDPGTPase KRas/0.608
4hdqGNPRas-related protein Rap-1b/0.607
3tgpGNPGTPase HRas/0.603
3lbhGNPGTPase HRas/0.602
4ldjGDPGTPase KRas/0.602
2fe4GDPRas-related protein Rab-6B/0.600
3kkoGNPRas-related protein M-Ras/0.599
3kkqGDPRas-related protein M-Ras/0.593
2rgeGNPGTPase HRas/0.591
2fg5GNPRas-related protein Rab-31/0.590
4o2rGDPGTP-binding protein Rheb/0.590
4ql3GDPGTPase KRas/0.588
3k9lGNPGTPase HRas/0.585
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.582
3ddcGNPGTPase HRas/0.581
3lbnGNPGTPase HRas/0.579
4xvrGNPGTPase HRas/0.575
3i3sGNPGTPase HRas/0.574
3rs4GNPGTPase HRas/0.572
3v4fGNPGTPase HRas/0.571
4dxaGSPRas-related protein Rap-1b/0.570
2cl6CAGGTPase HRas/0.564
2rgcGNPGTPase HRas/0.564
3k8yGNPGTPase HRas/0.563
4dlwGNPGTPase HRas/0.561
3x1wGDPRas-related protein Rap-1b/0.560
3qbtGNPRas-related protein Rab-8A/0.559
3rs5GNPGTPase HRas/0.558
4dlxGNPGTPase HRas/0.558
2rgbGNPGTPase HRas/0.557
4l9wGNPGTPase HRas/0.557
3oivGNPGTPase HRas/0.556
4dlvGNPGTPase HRas/0.555
4dlzGNPGTPase HRas/0.555
4dsuGDPGTPase KRas/0.555
2mscGDPMHC class I alpha chain/0.553
4dltGNPGTPase HRas/0.551
5dhaGNPGTP-binding nuclear protein Ran/0.550
2bmeGNPRas-related protein Rab-4A/0.548
2c5lGTPGTPase HRas/0.547
3oiwGNPGTPase HRas/0.547
5jljGNPGTP-binding nuclear protein Ran/0.547
3lbiGNPGTPase HRas/0.546
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.546
3pitGNPRas-related protein M-Ras/0.545
3tsoGNPRas-related protein Rab-25/0.544
3l8yGNPGTPase HRas/0.543
3rs0GNPGTPase HRas/0.543
4dsnGCPGTPase KRas/0.543
4g0nGNPGTPase HRas/0.541
4nyjGNPGTPase HRas/0.539
4cidANPEH domain-containing protein 2/0.537
5difGNPGTP-binding nuclear protein Ran/0.537
1xtsGTPGTP-binding protein Rheb/0.530
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.530
3x1zGNPRas-related protein Rap-1b/0.526
1zc4GNPRas-related protein Ral-A/0.523
4dlsGNPGTPase HRas/0.522
1e96GTPRas-related C3 botulinum toxin substrate 1/0.519
3a58GNPGTP-binding protein RHO1/0.519
3oiuGNPGTPase HRas/0.519
4lhwGNPRas-related protein Rab-8A/0.518
1kmqGNPTransforming protein RhoA/0.517
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.517
3rslGNPGTPase HRas/0.516
3kudGDPGTPase HRas/0.515
1lfdGNPGTPase HRas/0.514
5b2zGNPGTPase HRas/0.511
1n6lGTPRas-related protein Rab-5A/0.508
1yu9GNPRas-related protein Rab-4A/0.507
3e5hGNPRas-related protein Rab-28/0.506
4rkfGNPRas-related protein Rab-3/0.506
4dsoGSPGTPase KRas/0.504
1z2aGDPRas-related protein Rab-23/0.503
3rs7GNPGTPase HRas/0.503
1x1rGDPRas-related protein M-Ras/0.502
4qxaGTPRas-related protein Rab-9A/0.502
3cphGDPRas-related protein SEC4/0.501
4o2lGTPGTP-binding protein Rheb/0.501
4uj5GNPRas-related protein Rab-11A/0.501
1d5cGDPGTPase (Rab6)/0.497
1zbdGTPRas-related protein Rab-3A/0.496
3kucGDPRas-related protein Rap-1A/0.496
1tu3GNPRas-related protein Rab-5A/0.494
1oixGDPRas-related protein Rab-11A/0.493
5iqaGNPBifunctional AAC/APH2.3.10.493
3mjhGTPRas-related protein Rab-5A/0.492
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.491
2bkuGTPGTP-binding nuclear protein Ran/0.490
3oesGNPGTPase RhebL1/0.489
1a2bGSPTransforming protein RhoA/0.488
3a6pGTPGTP-binding nuclear protein Ran/0.488
4uj3GNPRas-related protein Rab-11A/0.488
4hdoGNPRas-related protein Rap-1b/0.486
5iqbGNPBifunctional AAC/APH2.3.10.486
3bbpGTPRas-related protein Rab-6A/0.485
1gwnGTPRho-related GTP-binding protein RhoE/0.482
1ii6ADPKinesin-like protein KIF11/0.478
2mseGNPMHC class I alpha chain/0.478
1yhnGTPRas-related protein Rab-7a/0.477
2gcpGSPRho-related GTP-binding protein RhoC/0.476
5iqdGNPBifunctional AAC/APH2.3.10.476
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.475
3kz1GSPTransforming protein RhoA/0.475
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.475
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.474
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.473
1k5dGNPGTP-binding nuclear protein Ran/0.472
1v8kANPKinesin-like protein KIF2C/0.472
1xtrGNPGTP-binding protein Rheb/0.471
3w3zGTPGTP-binding nuclear protein Ran/0.471
2msdGNPMHC class I alpha chain/0.470
4tzt468Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
1m7bGTPRho-related GTP-binding protein RhoE/0.469
2q3fGNPRas-related GTP-binding protein D/0.469
3gkjHC3Niemann-Pick C1 protein/0.469
3vhxGTPADP-ribosylation factor 6/0.469
3wyfGTPGTP-binding nuclear protein/0.469
1ky2GNPGTP-binding protein YPT7/0.468
4u0k744Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.468
2c29NAPDihydroflavonol 4-reductase/0.466
4js0GNPCell division control protein 42 homolog/0.465
5iu86DZAdenosine receptor A2a/0.465
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.464
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.464
1n83CLRNuclear receptor ROR-alpha/0.463
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.462
1a4rGNHCell division control protein 42 homolog/0.461
1ow3GDPTransforming protein RhoA/0.460
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.460
2gzl2AA2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.460
3fnhJPJEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
3ictADPCoenzyme A disulfide reductase/0.460
1vg8GNPRas-related protein Rab-7a/0.457
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.456
4ag7COAGlucosamine 6-phosphate N-acetyltransferase/0.456
1z0dGDPRas-related protein Rab-5C/0.455
3th5GNPRas-related C3 botulinum toxin substrate 1/0.455
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.455
1x2hLPALipoate-protein ligase A6.3.1.200.454
5hpyGDPTransforming protein RhoA/0.454
1g16GDPRas-related protein SEC4/0.453
2wu5CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.453
2wu5CBESuccinate dehydrogenase cytochrome b556 subunit/0.453
3bi6396Wee1-like protein kinase2.7.10.20.453
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
4hw219HInduced myeloid leukemia cell differentiation protein Mcl-1/0.453
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.451
2ffqGSPRas-related protein Rab-6B/0.451
2vprTDCTetracycline repressor protein class H/0.451
4cjqVXOIntegrase/0.451
5k2bZMAAdenosine receptor A2a/0.451
1s0xC3SNuclear receptor ROR-alpha/0.450
2j0vGDPRac-like GTP-binding protein ARAC7/0.449
2vo4GTB2,4-D inducible glutathione S-transferase/0.449
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.449
4mitGTPRho-related protein racC/0.449
2bxmIMNSerum albumin/0.448
3x2fNAIAdenosylhomocysteinase/0.448
5iqeGNPBifunctional AAC/APH2.3.10.448
3emlZMAAdenosine receptor A2a/0.448
2xvw9NRSerum albumin/0.447
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.447
4djx0KQBeta-secretase 13.4.23.460.447
1poxFADPyruvate oxidase1.2.3.30.446
2cbsR13Cellular retinoic acid-binding protein 2/0.446
2vcmM11Isopenicillin N synthase1.21.3.10.446
4fidGDPG protein alpha subunit, putative/0.446
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.446
5uviZMAAdenosine receptor A2a/0.446
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.445
3ea5GDPGTP-binding nuclear protein Ran/0.445
4pnmNU1Tankyrase-22.4.2.300.445
5di3GNPADP-ribosylation factor-like protein 3/0.445
5iubCLRAdenosine receptor A2a/0.445
1efvFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.444
5bylGCPBifunctional AAC/APH2.3.10.444
5iqgGDPBifunctional AAC/APH2.3.10.444
5iqiGNPBifunctional AAC/APH2.3.10.444
5k2cZMAAdenosine receptor A2a/0.444
1wdtGTPElongation factor G (EF-G-2)/0.443
2pupADPMethylthioribose kinase2.7.1.1000.443
3up3XCAaceDAF-12/0.443
4kvgGTPRas-related protein Rap-1A/0.443
2bbqPFGThymidylate synthase/0.442
3d84NDPDihydrofolate reductase1.5.1.30.442
4pkl1GHUncharacterized protein/0.442
5il1SAMN6-adenosine-methyltransferase 70 kDa subunit/0.442
5kf2COAPredicted acetyltransferase/0.442
2c3p1TPPyruvate synthase/0.441
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
2xvv9DNSerum albumin/0.441
3q5dGDPAtlastin-13.6.50.441
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.440
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.440
3b9lAZZSerum albumin/0.440
4ceqQCHIntegrase/0.440
4g01GDPRas-related protein RABF2b/0.440
4p9dTMPDeoxycytidylate deaminase/0.440