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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2fg5GNPRas-related protein Rab-31

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2fg5GNPRas-related protein Rab-31/1.000
3mjhGTPRas-related protein Rab-5A/0.589
2fe4GDPRas-related protein Rab-6B/0.556
1n6lGTPRas-related protein Rab-5A/0.552
4o2rGDPGTP-binding protein Rheb/0.550
4tq9GDPGTPase KRas/0.548
1tu3GNPRas-related protein Rab-5A/0.545
4l8gGDPGTPase KRas/0.543
2q3fGNPRas-related GTP-binding protein D/0.541
4hdqGNPRas-related protein Rap-1b/0.539
3cphGDPRas-related protein SEC4/0.537
4d0lGSPRas-related protein Rab-11A/0.537
5c46GSPRas-related protein Rab-11A/0.537
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.534
5dhaGNPGTP-binding nuclear protein Ran/0.533
1ky2GNPGTP-binding protein YPT7/0.532
4l9sGDPGTPase HRas/0.532
3a6pGTPGTP-binding nuclear protein Ran/0.531
3qbtGNPRas-related protein Rab-8A/0.530
3tgpGNPGTPase HRas/0.527
4xvrGNPGTPase HRas/0.526
3kkqGDPRas-related protein M-Ras/0.525
3tsoGNPRas-related protein Rab-25/0.523
4qxaGTPRas-related protein Rab-9A/0.522
1xtsGTPGTP-binding protein Rheb/0.521
1z2aGDPRas-related protein Rab-23/0.521
1zd9GDPADP-ribosylation factor-like protein 8A/0.521
3vhxGTPADP-ribosylation factor 6/0.520
4lucGDPGTPase KRas/0.520
1ibrGNPGTP-binding nuclear protein Ran/0.519
2rggGNPGTPase HRas/0.519
1z0dGDPRas-related protein Rab-5C/0.517
4uj3GNPRas-related protein Rab-11A/0.516
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.515
4epxGDPGTPase KRas/0.514
4lpkGDPGTPase KRas/0.513
4obeGDPGTPase KRas/0.512
1x1rGDPRas-related protein M-Ras/0.510
1yu9GNPRas-related protein Rab-4A/0.508
2gilGTPRas-related protein Rab-6A/0.508
4q03GDPGTPase KRas/0.507
5di3GNPADP-ribosylation factor-like protein 3/0.507
3rabGNPRas-related protein Rab-3A/0.506
4epwGDPGTPase KRas/0.505
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.504
4lrwGDPGTPase KRas/0.504
4uj5GNPRas-related protein Rab-11A/0.503
4xvqGNPGTPase HRas/0.503
1k5dGNPGTP-binding nuclear protein Ran/0.502
1d5cGDPGTPase (Rab6)/0.499
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.499
4ql3GDPGTPase KRas/0.499
4lv6GDPGTPase KRas/0.498
4nyjGNPGTPase HRas/0.497
3kkoGNPRas-related protein M-Ras/0.496
1yzqGNPRas-related protein Rab-6A/0.494
1zbdGTPRas-related protein Rab-3A/0.494
4o25GTPGTP-binding protein Rheb/0.494
3qe0GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.493
2bmeGNPRas-related protein Rab-4A/0.492
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.492
3pitGNPRas-related protein M-Ras/0.491
4fidGDPG protein alpha subunit, putative/0.491
4ldjGDPGTPase KRas/0.491
5jljGNPGTP-binding nuclear protein Ran/0.491
1oixGDPRas-related protein Rab-11A/0.490
4wa7GDPGTPase KRas/0.490
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.489
3e5hGNPRas-related protein Rab-28/0.489
4ol0GTPGTP-binding nuclear protein Ran/0.489
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.488
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.487
3lbhGNPGTPase HRas/0.487
3w3zGTPGTP-binding nuclear protein Ran/0.487
3wyfGTPGTP-binding nuclear protein/0.487
4lhwGNPRas-related protein Rab-8A/0.486
4q02GDPGTPase KRas/0.486
4yjdFADD-amino-acid oxidase1.4.3.30.485
1xtrGNPGTP-binding protein Rheb/0.484
1uadGNPRas-related protein Ral-A/0.483
3v4fGNPGTPase HRas/0.483
4cidANPEH domain-containing protein 2/0.483
4rkfGNPRas-related protein Rab-3/0.483
2zetGTPRas-related protein Rab-27B/0.482
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.482
3t1tGDPProbable gliding protein mglA/0.482
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.482
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.481
3ddcGNPGTPase HRas/0.481
4nyiGNPGTPase HRas/0.481
1z0aGDPRas-related protein Rab-2A/0.480
4xg1LLPDiaminopimelate decarboxylase/0.479
3k9lGNPGTPase HRas/0.478
3tklGTPRas-related protein Rab-1A/0.477
4dsnGCPGTPase KRas/0.477
1e96GTPRas-related C3 botulinum toxin substrate 1/0.476
2c5lGTPGTPase HRas/0.476
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.476
3nbzGTPGTP-binding nuclear protein Ran/0.476
3oesGNPGTPase RhebL1/0.476
4g0nGNPGTPase HRas/0.476
4gojGNPADP-ribosylation factor-like protein 3/0.473
2rcyNAPPyrroline-5-carboxylate reductase/0.472
4hdoGNPRas-related protein Rap-1b/0.472
4o2lGTPGTP-binding protein Rheb/0.471
1t91GTPRas-related protein Rab-7a/0.469
2dftADPShikimate kinase2.7.1.710.469
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.469
3k8yGNPGTPase HRas/0.469
1vg8GNPRas-related protein Rab-7a/0.466
2gvdGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.466
2ce2GDPGTPase HRas/0.465
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.465
2rgbGNPGTPase HRas/0.465
3oiuGNPGTPase HRas/0.465
4dptAGSMevalonate diphosphate decarboxylase/0.465
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.465
4js0GNPCell division control protein 42 homolog/0.465
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.464
3ea5GDPGTP-binding nuclear protein Ran/0.464
3lawGNPRas-related protein Rab-7a/0.464
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.464
3x1zGNPRas-related protein Rap-1b/0.464
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.463
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.463
1wdtGTPElongation factor G (EF-G-2)/0.462
3lbnGNPGTPase HRas/0.462
1g17GNPRas-related protein SEC4/0.461
2cl6CAGGTPase HRas/0.461
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.461
3x1wGDPRas-related protein Rap-1b/0.461
4dlwGNPGTPase HRas/0.461
1h2bNAJNAD-dependent alcohol dehydrogenase/0.460
3b70NAPEnoyl reductase LovC10.460
4g01GDPRas-related protein RABF2b/0.460
2ahrNAPPyrroline-5-carboxylate reductase/0.459
3tjzGNPADP-ribosylation factor 1/0.459
1dr2TAPDihydrofolate reductase1.5.1.30.458
3bbpGTPRas-related protein Rab-6A/0.458
3pcrGTPADP-ribosylation factor 6/0.458
2gjlFMNNitronate monooxygenase1.13.12.160.457
3iw1ASDSteroid C26-monooxygenase1.14.13.1410.457
3r7wGNPGTP-binding protein GTR2/0.457
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.457
2rgcGNPGTPase HRas/0.456
2rgeGNPGTPase HRas/0.456
3eg5GNPCell division control protein 42 homolog/0.456
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4itrGDPCell division control protein 42 homolog/0.456
1lfdGNPGTPase HRas/0.455
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.455
1ykdCMPAdenylate cyclase/0.455
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.455
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.455
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.455
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.455
5dozNDPJamJ/0.455
1kmqGNPTransforming protein RhoA/0.454
1xkqNDPUncharacterized protein/0.454
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.454
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
3nxxNDPDihydrofolate reductase1.5.1.30.454
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.454
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.454
1dr3TAPDihydrofolate reductase1.5.1.30.453
1u33LM2Pancreatic alpha-amylase/0.453
1uxjNADMalate dehydrogenase/0.453
2bxqIMNSerum albumin/0.453
2ffqGSPRas-related protein Rab-6B/0.453
2mscGDPMHC class I alpha chain/0.453
3jvvACPTwitching mobility protein/0.453
4dltGNPGTPase HRas/0.453
4f6w0SSCyclin-dependent kinase 82.7.11.220.453
5hpyGDPTransforming protein RhoA/0.453
1zc4GNPRas-related protein Ral-A/0.452
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
2ylrNAPPhenylacetone monooxygenase1.14.13.920.452
4du82P0Mevalonate diphosphate decarboxylase/0.452
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
1juvNDPDihydrofolate reductase1.5.1.30.451
1u2oNECEndoplasmin/0.451
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.451
1zcbGDPGuanine nucleotide-binding protein subunit alpha-13/0.451
2j0vGDPRac-like GTP-binding protein ARAC7/0.451
2vhzNAIAlanine dehydrogenase1.4.1.10.451
2zevB71Geranylgeranyl pyrophosphate synthase/0.451
3refGDPRho family GTPase/0.451
4ead0NPThymidine phosphorylase2.4.2.40.451
4mitGTPRho-related protein racC/0.451
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.450
3tqaNDPDihydrofolate reductase/0.450
5b2zGNPGTPase HRas/0.450
1e79ATPATP synthase subunit alpha, mitochondrial/0.449
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.449
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.449
2xtnGTPGTPase IMAP family member 2/0.449
3gwdNAPCyclohexanone monooxygenase/0.449
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
3kucGDPRas-related protein Rap-1A/0.449
3oiwGNPGTPase HRas/0.449
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.449
3rs4GNPGTPase HRas/0.449
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.449
1dr5NAPDihydrofolate reductase1.5.1.30.448
1s1cGNPTransforming protein RhoA/0.448
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.448
3rs5GNPGTPase HRas/0.448
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.448
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.448
5difGNPGTP-binding nuclear protein Ran/0.448
1oc1ASVIsopenicillin N synthase1.21.3.10.447
3gqvNAPEnoyl reductase LovC10.447
4dxaGSPRas-related protein Rap-1b/0.447
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.447
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.446
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
3eldSFGMethyltransferase/0.446
3f63GTXGlutathione transferase GST1-4/0.446
3qlsNDPDihydrofolate reductase1.5.1.30.446
3rkuNAPNADP-dependent 3-hydroxy acid dehydrogenase/0.446
3th5GNPRas-related C3 botulinum toxin substrate 1/0.446
4dsuGDPGTPase KRas/0.446
4k81GTPGTPase HRas/0.446
1g16GDPRas-related protein SEC4/0.445
2a94AP0L-lactate dehydrogenase1.1.1.270.445
2bkuGTPGTP-binding nuclear protein Ran/0.445
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.445
2q29ACOOxalyl-CoA decarboxylase4.1.1.80.445
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.445
3oivGNPGTPase HRas/0.445
3rslGNPGTPase HRas/0.445
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.445
1pqc444Oxysterols receptor LXR-beta/0.444
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4xyeNADFormate dehydrogenase/0.444
1a4rGNHCell division control protein 42 homolog/0.443
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.443
1u0hGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.443
2fsvNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.443
3f3sNADLambda-crystallin homolog/0.443
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.443
4xoiGTPTransforming protein RhoA/0.443
1am4GNPCell division control protein 42 homolog/0.442
1beuIPLTryptophan synthase alpha chain/0.442
1fduNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1g6oADPCag alpha/0.442
1guyNADMalate dehydrogenase/0.442
1hk3T44Serum albumin/0.442
1xddAAYIntegrin alpha-L/0.442
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
2h2eSA8Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.442
2q9fC3SCholesterol 24-hydroxylase/0.442
2ym1FADPhenylacetone monooxygenase1.14.13.920.442
3ijoB4DGlutamate receptor 2/0.442
3pefNAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase/0.442
4bfuZVUPantothenate kinase2.7.1.330.442
1eioGCHGastrotropin/0.441
1zeoC01Peroxisome proliferator-activated receptor gamma/0.441
2c29NAPDihydroflavonol 4-reductase/0.441
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.441
2xlrNAPPutative flavin-containing monooxygenase/0.441
2zjaACPATP-dependent DNA helicase Hel308/0.441
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.441
3p19NDPPutative blue fluorescent protein/0.441
3pqbVGPPutative oxidoreductase/0.441
3r9xGNPGTPase Era/0.441
3rs0GNPGTPase HRas/0.441
3s87ADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.441
4bfvZVVPantothenate kinase2.7.1.330.441
4dlzGNPGTPase HRas/0.441
4z24FADPutative GMC-type oxidoreductase R13510.441
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.441
1obnASVIsopenicillin N synthase1.21.3.10.440
1p44NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
1qy5NECEndoplasmin/0.440
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.440
3jzdNADMaleylacetate reductase/0.440
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.440
3wleNAD(R)-specific carbonyl reductase/0.440
4a5lNDPThioredoxin reductase/0.440
4dc0NDPPutative ketoacyl reductase1.3.10.440
4q71FADBifunctional protein PutA/0.440
4wfr2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
5fm7ADPRuvB-like helicase/0.440