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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
4lv6GDPGTPase KRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4lv6GDPGTPase KRas/1.000
4tq9GDPGTPase KRas/0.684
4l8gGDPGTPase KRas/0.666
4lpkGDPGTPase KRas/0.663
4q02GDPGTPase KRas/0.658
4l9sGDPGTPase HRas/0.654
3kkqGDPRas-related protein M-Ras/0.648
2ce2GDPGTPase HRas/0.647
2rggGNPGTPase HRas/0.647
4q03GDPGTPase KRas/0.647
4epxGDPGTPase KRas/0.641
4obeGDPGTPase KRas/0.636
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.633
4wa7GDPGTPase KRas/0.633
4epwGDPGTPase KRas/0.619
1x1rGDPRas-related protein M-Ras/0.616
4lrwGDPGTPase KRas/0.614
4ldjGDPGTPase KRas/0.613
4hdqGNPRas-related protein Rap-1b/0.609
4ql3GDPGTPase KRas/0.607
3rs0GNPGTPase HRas/0.606
3lbnGNPGTPase HRas/0.603
1n6lGTPRas-related protein Rab-5A/0.602
3rs4GNPGTPase HRas/0.602
3tgpGNPGTPase HRas/0.602
4o2rGDPGTP-binding protein Rheb/0.601
3kkoGNPRas-related protein M-Ras/0.600
4g0nGNPGTPase HRas/0.597
2fe4GDPRas-related protein Rab-6B/0.596
4dlsGNPGTPase HRas/0.595
3tsoGNPRas-related protein Rab-25/0.594
3rs7GNPGTPase HRas/0.588
4nyiGNPGTPase HRas/0.585
2rgeGNPGTPase HRas/0.584
3k9lGNPGTPase HRas/0.584
3i3sGNPGTPase HRas/0.581
3lbhGNPGTPase HRas/0.579
4xvqGNPGTPase HRas/0.579
1g17GNPRas-related protein SEC4/0.578
3x1wGDPRas-related protein Rap-1b/0.578
2rgcGNPGTPase HRas/0.577
3qbtGNPRas-related protein Rab-8A/0.577
3v4fGNPGTPase HRas/0.577
4dlzGNPGTPase HRas/0.577
4dsuGDPGTPase KRas/0.575
3lbiGNPGTPase HRas/0.574
4nyjGNPGTPase HRas/0.574
2rgbGNPGTPase HRas/0.573
4dltGNPGTPase HRas/0.572
4dsnGCPGTPase KRas/0.571
4lhwGNPRas-related protein Rab-8A/0.571
3ddcGNPGTPase HRas/0.570
1zd9GDPADP-ribosylation factor-like protein 8A/0.569
2fg5GNPRas-related protein Rab-31/0.569
3cphGDPRas-related protein SEC4/0.569
4xvrGNPGTPase HRas/0.568
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.567
3pitGNPRas-related protein M-Ras/0.566
3rslGNPGTPase HRas/0.565
4l9wGNPGTPase HRas/0.565
5dhaGNPGTP-binding nuclear protein Ran/0.565
1cxzGSPTransforming protein RhoA/0.564
1uadGNPRas-related protein Ral-A/0.564
4dlxGNPGTPase HRas/0.564
2mscGDPMHC class I alpha chain/0.561
3x1zGNPRas-related protein Rap-1b/0.561
4dlvGNPGTPase HRas/0.561
3k8yGNPGTPase HRas/0.556
4dsoGSPGTPase KRas/0.556
3oiuGNPGTPase HRas/0.555
2cl6CAGGTPase HRas/0.554
1lfdGNPGTPase HRas/0.553
3l8yGNPGTPase HRas/0.552
1yzqGNPRas-related protein Rab-6A/0.551
2c5lGTPGTPase HRas/0.550
3a58GNPGTP-binding protein RHO1/0.548
4dlwGNPGTPase HRas/0.548
4uj3GNPRas-related protein Rab-11A/0.548
3oivGNPGTPase HRas/0.547
3oiwGNPGTPase HRas/0.546
5difGNPGTP-binding nuclear protein Ran/0.546
1oixGDPRas-related protein Rab-11A/0.545
1kmqGNPTransforming protein RhoA/0.544
2bmeGNPRas-related protein Rab-4A/0.543
3kudGDPGTPase HRas/0.542
4qxaGTPRas-related protein Rab-9A/0.542
1xtsGTPGTP-binding protein Rheb/0.541
1zc4GNPRas-related protein Ral-A/0.541
1d5cGDPGTPase (Rab6)/0.538
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.537
3rs5GNPGTPase HRas/0.534
4dxaGSPRas-related protein Rap-1b/0.534
4rkfGNPRas-related protein Rab-3/0.534
2ffqGSPRas-related protein Rab-6B/0.532
3oesGNPGTPase RhebL1/0.531
1t91GTPRas-related protein Rab-7a/0.530
1yu9GNPRas-related protein Rab-4A/0.530
1zbdGTPRas-related protein Rab-3A/0.530
4hdoGNPRas-related protein Rap-1b/0.528
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.527
2gcpGSPRho-related GTP-binding protein RhoC/0.526
1a2bGSPTransforming protein RhoA/0.520
3kucGDPRas-related protein Rap-1A/0.515
3mjhGTPRas-related protein Rab-5A/0.515
3vhxGTPADP-ribosylation factor 6/0.515
1e96GTPRas-related C3 botulinum toxin substrate 1/0.514
4o2lGTPGTP-binding protein Rheb/0.514
5di3GNPADP-ribosylation factor-like protein 3/0.514
5jljGNPGTP-binding nuclear protein Ran/0.514
2msdGNPMHC class I alpha chain/0.513
1z0dGDPRas-related protein Rab-5C/0.512
2bkuGTPGTP-binding nuclear protein Ran/0.512
4cidANPEH domain-containing protein 2/0.511
1ow3GDPTransforming protein RhoA/0.510
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.509
1g16GDPRas-related protein SEC4/0.508
2q3fGNPRas-related GTP-binding protein D/0.508
3kz1GSPTransforming protein RhoA/0.508
1vg8GNPRas-related protein Rab-7a/0.507
4mitGTPRho-related protein racC/0.507
3pcrGTPADP-ribosylation factor 6/0.505
5b2zGNPGTPase HRas/0.505
3ea5GDPGTP-binding nuclear protein Ran/0.503
3eg5GNPCell division control protein 42 homolog/0.502
1z2aGDPRas-related protein Rab-23/0.500
3a6pGTPGTP-binding nuclear protein Ran/0.499
3rabGNPRas-related protein Rab-3A/0.499
1fw0KAIGlutamate receptor 2/0.497
3e5hGNPRas-related protein Rab-28/0.497
3w3zGTPGTP-binding nuclear protein Ran/0.497
1yhnGTPRas-related protein Rab-7a/0.495
1xtrGNPGTP-binding protein Rheb/0.493
4o25GTPGTP-binding protein Rheb/0.493
1ky2GNPGTP-binding protein YPT7/0.491
3bbpGTPRas-related protein Rab-6A/0.491
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.490
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.490
5hpyGDPTransforming protein RhoA/0.490
1a4rGNHCell division control protein 42 homolog/0.489
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.486
1z2cGNPRho-related GTP-binding protein RhoC/0.485
4g01GDPRas-related protein RABF2b/0.485
1k5dGNPGTP-binding nuclear protein Ran/0.481
1n83CLRNuclear receptor ROR-alpha/0.481
4d0lGSPRas-related protein Rab-11A/0.480
3refGDPRho family GTPase/0.479
3wyfGTPGTP-binding nuclear protein/0.478
4js0GNPCell division control protein 42 homolog/0.478
1m7bGTPRho-related GTP-binding protein RhoE/0.477
5iqiGNPBifunctional AAC/APH2.3.10.477
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.476
2c29NAPDihydroflavonol 4-reductase/0.475
1ibrGNPGTP-binding nuclear protein Ran/0.474
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.474
3qcs3Q13-phosphoinositide-dependent protein kinase 12.7.11.10.474
1v8kANPKinesin-like protein KIF2C/0.473
4p9dTMPDeoxycytidylate deaminase/0.473
4y0vGDPADP-ribosylation factor 1, putative/0.472
3fnhJPJEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
4jauADPSensor histidine kinase/0.470
1gwnGTPRho-related GTP-binding protein RhoE/0.469
1xe65FPPlasmepsin-23.4.23.390.469
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.469
2e0nSAHPrecorrin-2 C20-methyltransferase/0.469
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.469
2mseGNPMHC class I alpha chain/0.468
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.468
1unhIXMCyclin-dependent-like kinase 52.7.11.10.466
2j0vGDPRac-like GTP-binding protein ARAC7/0.466
3nbzGTPGTP-binding nuclear protein Ran/0.466
4xymCOAAcyl-CoA synthetase (NDP forming)/0.466
2wu5CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.465
2wu5CBESuccinate dehydrogenase cytochrome b556 subunit/0.465
3pcnDHYProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.465
3pcnDHYProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.465
5iqdGNPBifunctional AAC/APH2.3.10.465
5iu86DZAdenosine receptor A2a/0.465
1ii6ADPKinesin-like protein KIF11/0.463
1pq944BOxysterols receptor LXR-beta/0.463
1z2nADPInositol-tetrakisphosphate 1-kinase2.7.1.1340.463
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.463
3rkuNAPNADP-dependent 3-hydroxy acid dehydrogenase/0.463
3up3XCAaceDAF-12/0.463
5iqgGDPBifunctional AAC/APH2.3.10.463
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.462
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.462
3nn6HNK6-hydroxy-L-nicotine oxidase/0.462
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.461
2z4sADPChromosomal replication initiator protein DnaA/0.461
4b722FBBeta-secretase 13.4.23.460.461
4bfvZVVPantothenate kinase2.7.1.330.461
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.461
4udqFAD5-(hydroxymethyl)furfural oxidase/0.460
1xzqFONtRNA modification GTPase MnmE3.6.50.459
3tkh07SSerine/threonine-protein kinase Chk12.7.11.10.459
4ehyADPTetraacyldisaccharide 4'-kinase/0.459
4j49NAIUncharacterized protein/0.459
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.458
2r9eSDXCitrate synthase2.3.3.160.458
1qjfACSIsopenicillin N synthase1.21.3.10.457
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.457
2gzl2AA2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.457
3th5GNPRas-related C3 botulinum toxin substrate 1/0.457
4gojGNPADP-ribosylation factor-like protein 3/0.457
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.457
4ylgGDPADP-ribosylation factor 1, putative/0.457
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.456
1juvNDPDihydrofolate reductase1.5.1.30.456
1m78NDPDihydrofolate reductase1.5.1.30.456
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.456
3cobADPKinesin heavy chain-like protein/0.456
3r7wGNPGTP-binding protein GTR2/0.456
4ehv0SJMitogen-activated protein kinase 14/0.456
2izsBRQCasein kinase I isoform gamma-32.7.11.10.455
2ji7ADPOxalyl-CoA decarboxylase4.1.1.80.455
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.455
2yg4FADPutrescine oxidase/0.455
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3ewsADPATP-dependent RNA helicase DDX19B3.6.4.130.455
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.455
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.454
4a5lNDPThioredoxin reductase/0.454
2ok8FADFerredoxin--NADP reductase, apicoplast/0.453
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.453
1npdNADQuinate/shikimate dehydrogenase/0.452
2c2aADPSensor histidine kinase/0.452
2yg3FADPutrescine oxidase/0.452
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.452
4tldAGSCircadian clock protein kinase KaiC2.7.11.10.452
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.452
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.451
5kbwRBFRiboflavin transporter RibU/0.451
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.450
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.450
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.450
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.450
4ol0GTPGTP-binding nuclear protein Ran/0.450
1g4tFTPThiamine-phosphate synthase/0.449
1rd4L08Integrin alpha-L/0.449
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
3d7zGK5Mitogen-activated protein kinase 14/0.449
3fhxPLPPyridoxal kinase2.7.1.350.449
3p74FMNPentaerythritol tetranitrate reductase/0.449
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.449
4pnmNU1Tankyrase-22.4.2.300.449
4z87GDPInosine-5'-monophosphate dehydrogenase/0.449
5iqbGNPBifunctional AAC/APH2.3.10.449
3sn6P0GBeta-2 adrenergic receptor/0.449
4coxIMNProstaglandin G/H synthase 21.14.99.10.448
5l3dFADLysine-specific histone demethylase 1A10.448
1poxFADPyruvate oxidase1.2.3.30.447
1vyrFMNPentaerythritol tetranitrate reductase/0.447
3qcy3Q33-phosphoinositide-dependent protein kinase 12.7.11.10.447
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.447
3t1tGDPProbable gliding protein mglA/0.447
3w10RO9Aurora kinase A2.7.11.10.447
4fidGDPG protein alpha subunit, putative/0.447
1bcpATPPertussis toxin subunit 4/0.446
1bcpATPPertussis toxin subunit 5/0.446
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.446
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.446
2wo7ASVIsopenicillin N synthase1.21.3.10.446
4iah1DXAlr2278 protein/0.446
5esoTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.446
5iqaGNPBifunctional AAC/APH2.3.10.446
1n08ADPRiboflavin kinase2.7.1.260.445
1xngDNDNH(3)-dependent NAD(+) synthetase6.3.1.50.445
1youPFDCollagenase 33.4.240.445
2g78REACellular retinoic acid-binding protein 2/0.445
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.445
3mohGDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.445
3phiNDPShikimate dehydrogenase (NADP(+))/0.445
4aw1ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.445
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.445
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.445
1efvFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.444
1rx8FOLDihydrofolate reductase1.5.1.30.444
2ftoCB3Thymidylate synthase/0.444
2owb626Serine/threonine-protein kinase PLK12.7.11.210.444
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3pvcFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.444
4cjqVXOIntegrase/0.444
4crzACOPanD regulatory factor/0.444
4f0e0RUPoly [ADP-ribose] polymerase 152.4.2.300.444
4mv1ADPBiotin carboxylase6.3.4.140.444
1pd9CO4Dihydrofolate reductase1.5.1.30.443
1qm5PLPMaltodextrin phosphorylase2.4.1.10.443
3vasADNPutative adenosine kinase/0.443
3x2fNAIAdenosylhomocysteinase/0.443
4bdrKAIGlutamate receptor ionotropic, kainate 2/0.443
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.443
1cdeDZFPhosphoribosylglycinamide formyltransferase/0.442
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.442
2r6jNDPEugenol synthase 11.1.1.3180.442
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.442
3nunJMZ3-phosphoinositide-dependent protein kinase 12.7.11.10.442
3oom507Activin receptor type-12.7.11.300.442
3t4eNADQuinate/shikimate dehydrogenase/0.442
4b5oACOAlpha-tubulin N-acetyltransferase 1/0.442
4fkj11KCyclin-dependent kinase 22.7.11.220.442
4m6jNDPDihydrofolate reductase1.5.1.30.442
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.442
1dr2TAPDihydrofolate reductase1.5.1.30.441
1flmFMNFMN-binding protein/0.441
1jscTPPAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.441
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.441
1mabADPATP synthase subunit beta, mitochondrial3.6.3.140.441
1wdtGTPElongation factor G (EF-G-2)/0.441
2wu2CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.441
2wu2CBESuccinate dehydrogenase cytochrome b556 subunit/0.441
3nga3NGCasein kinase II subunit alpha2.7.11.10.441
4b0532DBeta-secretase 13.4.23.460.441
4bixADPSensor histidine kinase CpxA/0.441
4h9753SDihydrofolate reductase1.5.1.30.441
4xcjADPHeat shock cognate 90 kDa protein/0.441
1mvsDTMDihydrofolate reductase1.5.1.30.440
1s3uTQDDihydrofolate reductase1.5.1.30.440
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.440
2hckQUETyrosine-protein kinase HCK2.7.10.20.440
2ociTYCValacyclovir hydrolase3.10.440
2p5fSAHDiphthine synthase/0.440
2xjjL81Heat shock protein HSP 90-alpha/0.440
3cwkREACellular retinoic acid-binding protein 2/0.440
3hmm855TGF-beta receptor type-12.7.11.300.440
3kwn23ZCathepsin S3.4.22.270.440
4a2aATPCell division protein FtsA/0.440
4ag5ADPType IV secretory pathway VirB4 components-like protein/0.440
4l8u9AZSerum albumin/0.440
4u7wNDPMxaA/0.440