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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
1bofGDPGuanine nucleotide-binding protein G(i) subunit alpha-1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1bofGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/1.000
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.523
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.522
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.521
3qe0GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.506
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.499
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.491
2qenADPWalker-Type ATPase/0.485
1sxjAGSReplication factor C subunit 1/0.484
2b53D23Cyclin-dependent kinase 22.7.11.220.484
1m2oGNPSmall COPII coat GTPase SAR13.6.50.482
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.480
4z875GPInosine-5'-monophosphate dehydrogenase/0.480
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.476
4k6mSAHGenome polyprotein/0.476
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.473
3hx4ANPCalmodulin-domain protein kinase 1/0.472
4g95OAGDihydrofolate reductase1.5.1.30.471
3fhxPLPPyridoxal kinase2.7.1.350.470
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.469
3cx8GSPGuanine nucleotide-binding protein subunit alpha-13/0.469
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
1g4tFTPThiamine-phosphate synthase/0.468
3ajrNADNDP-sugar epimerase/0.468
4nbwNADShort-chain dehydrogenase/reductase SDR/0.468
5ch7MD1DMSO reductase family type II enzyme, molybdopterin subunit/0.468
1drhNAPDihydrofolate reductase1.5.1.30.467
1nzdUPGDNA beta-glucosyltransferase/0.467
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.467
1u71MXADihydrofolate reductase1.5.1.30.466
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.466
3cx6GDPGuanine nucleotide-binding protein subunit alpha-13/0.466
2eh4SAHDiphthine synthase/0.465
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.465
2nv4SAMS-adenosyl-L-methionine-binding protein AF_0241/0.465
3dvlATPCircadian clock protein kinase KaiC2.7.11.10.465
3elySAHMethyltransferase/0.465
1kr2TADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.464
2an9GDPGuanylate kinase2.7.4.80.464
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.464
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
3tdj3TJGlutamate receptor 2/0.464
1meiXMPInosine-5'-monophosphate dehydrogenase/0.463
2pckSAHDiphthine synthase/0.463
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.463
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4gfvPRO_GLU_LEU_THR_PTRTyrosine-protein phosphatase non-receptor type 183.1.3.480.462
4h4yNAPBiphenyl dioxygenase ferredoxin reductase subunit/0.462
1x2hLPALipoate-protein ligase A6.3.1.200.461
3iw1ASDSteroid C26-monooxygenase1.14.13.1410.461
3uylTYDProbable NDP-rhamnosyltransferase/0.461
4gh5NADShort-chain dehydrogenase/reductase SDR/0.461
4i02CMPcAMP-activated global transcriptional regulator CRP/0.461
1orrNADCDP-paratose 2-epimerase/0.460
3eluSAMMethyltransferase/0.460
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.460
4jldADPAdenylate kinase/0.460
3w8eNAD3-hydroxybutyrate dehydrogenase/0.459
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.459
2cy0NAPShikimate dehydrogenase (NADP(+))/0.458
2owkSAHDiphthine synthase/0.458
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.458
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3nxxNDPDihydrofolate reductase1.5.1.30.458
1n3rGTPGTP cyclohydrolase 13.5.4.160.457
1rx8FOLDihydrofolate reductase1.5.1.30.457
2i5bADPPyridoxine kinase/0.457
2pd7FADVivid PAS protein VVD/0.457
2y05NAPProstaglandin reductase 1/0.457
4lol1YEStimulator of interferon genes protein/0.457
1rx1NAPDihydrofolate reductase1.5.1.30.456
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.456
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.456
2h2aDNDProbable nicotinate-nucleotide adenylyltransferase/0.456
3s55NADPutative short-chain dehydrogenase/reductase/0.456
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.456
1cs4FOKAdenylate cyclase type 2/0.455
1cs4FOKAdenylate cyclase type 5/0.455
1h73ANPHomoserine kinase2.7.1.390.455
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.455
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.455
2dhfDZFDihydrofolate reductase1.5.1.30.455
2el0SAHDiphthine synthase/0.455
2vttLZDCyclin-dependent kinase 22.7.11.220.455
3pfdFDAAcyl-CoA dehydrogenase FadE25/0.455
1meiMOAInosine-5'-monophosphate dehydrogenase/0.454
2dftADPShikimate kinase2.7.1.710.454
2ev9NAPShikimate dehydrogenase (NADP(+))/0.454
2pxaSAHGenome polyprotein2.7.7.480.454
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.454
2zawCAMCamphor 5-monooxygenase1.14.15.10.454
3vhxGTPADP-ribosylation factor 6/0.454
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.453
1dr3TAPDihydrofolate reductase1.5.1.30.453
2eh5SAHDiphthine synthase/0.453
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.453
2z6dFMNPhototropin-22.7.11.10.453
3b70NAPEnoyl reductase LovC10.453
5a3cNADSIR2 family protein/0.453
1cqp803Integrin alpha-L/0.452
1q1wFADPutidaredoxin reductase1.18.1.50.452
2fy4COACholine O-acetyltransferase2.3.1.60.452
2huvSAHDiphthine synthase/0.452
3dzkNMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.452
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.452
4b4vL34Bifunctional protein FolD/0.452
2b69NADUDP-glucuronic acid decarboxylase 14.1.1.350.451
2owgSAHDiphthine synthase/0.451
2qtvGNPSmall COPII coat GTPase SAR13.6.50.451
2xvu9DNSerum albumin/0.451
4dpy2P0Mevalonate diphosphate decarboxylase/0.451
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
4hxyNDPPlm1/0.451
1il0NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.450
1xe65FPPlasmepsin-23.4.23.390.450
2c12FADNitroalkane oxidase1.7.3.10.450
2pauD5M5'-deoxynucleotidase YfbR/0.450
3c1y2BADNA integrity scanning protein DisA/0.450
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.450
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.450
3vdqNAD3-hydroxybutyrate dehydrogenase/0.450
4fv7E94Mitogen-activated protein kinase 12.7.11.240.450
4m9aFDAAcyl-CoA dehydrogenase/0.450
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.449
1ebdFADDihydrolipoyl dehydrogenase1.8.1.40.449
1nzfUPGDNA beta-glucosyltransferase/0.449
1o9bNAIQuinate/shikimate dehydrogenase/0.449
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.449
2briANPUridylate kinase2.7.4.220.449
2hxl422Serine/threonine-protein kinase Chk12.7.11.10.449
2p6lSAHDiphthine synthase/0.449
2xlrFADPutative flavin-containing monooxygenase/0.449
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.449
3juqAJDPhenazine biosynthesis protein A/B/0.449
3q1fYPPBeta-lactamase/0.449
3zidGDPTubulin-like protein CetZ/0.449
4e5pNADPhosphonate dehydrogenase1.20.1.10.449
4giu636Anthranilate phosphoribosyltransferase/0.449
4m11MXMProstaglandin G/H synthase 21.14.99.10.449
4udrFAD5-(hydroxymethyl)furfural oxidase/0.449
5a3bAPRSIR2 family protein/0.449
5kwvANPPantothenate synthetase/0.449
1h22E10Acetylcholinesterase3.1.1.70.448
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.448
1lc3NADBiliverdin reductase A1.3.1.240.448
1p9wANPType II secretion system protein E/0.448
1ra8FOLDihydrofolate reductase1.5.1.30.448
1rx8NAPDihydrofolate reductase1.5.1.30.448
1xddAAYIntegrin alpha-L/0.448
2aa3AP0L-lactate dehydrogenase/0.448
2cgx3D3Serine/threonine-protein kinase Chk12.7.11.10.448
2oapANPType II secretion system protein (GspE-2)/0.448
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.448
3oafOAGDihydrofolate reductase1.5.1.30.448
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.448
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.448
4du82P0Mevalonate diphosphate decarboxylase/0.448
4gk3L87Ephrin type-A receptor 32.7.10.10.448
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.448
1m75CAAHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.447
1u3dFADCryptochrome-1/0.447
1xelUPGUDP-glucose 4-epimerase5.1.3.20.447
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.447
2emrSAHDiphthine synthase/0.447
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.447
3eldSFGMethyltransferase/0.447
3p2oNADBifunctional protein FolD/0.447
3pcrGTPADP-ribosylation factor 6/0.447
3qsaTA7Anthranilate phosphoribosyltransferase/0.447
3qt62P0Mevalonate diphosphate decarboxylase/0.447
4dbzNDPPutative ketoacyl reductase1.3.10.447
4dmmNAP3-oxoacyl-[acyl-carrier-protein] reductase/0.447
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.447
4yagNAIC alpha-dehydrogenase/0.447
4zohFADPutative oxidoreductase FAD-binding subunit/0.447
5cyoGDPSeptin-9/0.447
5jjsSAHGenome polyprotein/0.447
1g1aNADdTDP-glucose 4,6-dehydratase/0.446
1rj9GCPSignal recognition particle receptor FtsY/0.446
2a94AP0L-lactate dehydrogenase1.1.1.270.446
2e7rSAHDiphthine synthase/0.446
2ek2SAHDiphthine synthase/0.446
2ek3SAHDiphthine synthase/0.446
2jn3JN3Fatty acid-binding protein, liver/0.446
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.446
3clrFADElectron transfer flavoprotein subunit alpha/0.446
3phiNDPShikimate dehydrogenase (NADP(+))/0.446
3r9iADPSeptum site-determining protein MinD/0.446
4dptAGSMevalonate diphosphate decarboxylase/0.446
1a8rGTPGTP cyclohydrolase 13.5.4.160.445
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.445
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.445
1pdhFASp-hydroxybenzoate hydroxylase/0.445
1tllNAPNitric oxide synthase, brain1.14.13.390.445
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.445
1w6hTITPlasmepsin-23.4.23.390.445
1wngSAHDiphthine synthase/0.445
1xkdNAPIsocitrate dehydrogenase [NADP]/0.445
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.445
2cig1DGDihydrofolate reductase1.5.1.30.445
2zbaZBATrichothecene 3-O-acetyltransferase/0.445
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.445
3t4eNADQuinate/shikimate dehydrogenase/0.445
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.445
4jqh1MFAlr2278 protein/0.445
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.445
4ztvTA7Anthranilate phosphoribosyltransferase/0.445
1bdbNADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase/0.444
1in5ADPHolliday junction ATP-dependent DNA helicase RuvB/0.444
1iy8NADLevodione reductase/0.444
1u0hGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.444
1udaUFGUDP-glucose 4-epimerase5.1.3.20.444
2dshSAHDiphthine synthase/0.444
2e15SAHDiphthine synthase/0.444
2e8hSAHDiphthine synthase/0.444
2nniMTKCytochrome P450 2C8/0.444
2ooyATP5'-AMP-activated protein kinase subunit gamma/0.444
2q4bNAPUncharacterized protein At5g02240/0.444
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.444
3nl6TPSUncharacterized protein/0.444
3tjzGNPADP-ribosylation factor 1/0.444
4a802ANMajor pollen allergen Bet v 1-A/0.444
4dzzADPPlasmid partitioning protein ParF/0.444
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.444
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.444
4xgxADPFAD:protein FMN transferase/0.444
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
1d4dFADFumarate reductase flavoprotein subunit1.3.5.40.443
1gcoNADGlucose 1-dehydrogenase1.1.1.470.443
1nf7RVPInosine-5'-monophosphate dehydrogenase 2/0.443
1pd9CO4Dihydrofolate reductase1.5.1.30.443
1xnjADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.443
2en5SAHDiphthine synthase/0.443
2tpsTPSThiamine-phosphate synthase/0.443
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.443
3qs817DAnthranilate phosphoribosyltransferase/0.443
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.443
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.443
4ji91M3Tyrosine-protein kinase JAK2/0.443
1f8fNADBenzyl alcohol dehydrogenase/0.442
1n1dC2GGlycerol-3-phosphate cytidylyltransferase2.7.7.390.442
1okkGCPSignal recognition particle protein/0.442
1okkGCPSignal recognition particle receptor FtsY/0.442
1touB1VFatty acid-binding protein, adipocyte/0.442
1towCRZFatty acid-binding protein, adipocyte/0.442
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.442
2pcmSAHDiphthine synthase/0.442
2rirNAPDipicolinate synthase subunit A/0.442
2tprFADTrypanothione reductase1.8.1.120.442
2vhwNAIAlanine dehydrogenase1.4.1.10.442
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.442
3vw6IM6Mitogen-activated protein kinase kinase kinase 52.7.11.250.442
4c04SFGProtein arginine N-methyltransferase 6/0.442
4d81ADPAAA ATPase, central domain protein/0.442
4dx7DM2Multidrug efflux pump subunit AcrB/0.442
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.442
4r1lADPPhenylacetate-coenzyme A ligase/0.442
1b8vNADMalate dehydrogenase/0.441
1cjtFOKAdenylate cyclase type 2/0.441
1cjtFOKAdenylate cyclase type 5/0.441
1guyNADMalate dehydrogenase/0.441
1u3cFADCryptochrome-1/0.441
2dsgSAHDiphthine synthase/0.441
2e16SAHDiphthine synthase/0.441
2e4nSAHDiphthine synthase/0.441
2fj1CTCTetracycline repressor protein class D/0.441
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.441
2p5cSAHDiphthine synthase/0.441
2pb6SAHDiphthine synthase/0.441
2z6iFMN2-nitropropane dioxygenase/0.441
2ztlNADD(-)-3-hydroxybutyrate dehydrogenase/0.441
3b6pTMPThree-prime repair exonuclease 13.1.11.20.441
4ft3H1KSerine/threonine-protein kinase Chk12.7.11.10.441
4h4wNAPBiphenyl dioxygenase ferredoxin reductase subunit/0.441
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.441
4nmdFDABifunctional protein PutA/0.441
4w6z8IDAlcohol dehydrogenase 11.1.1.10.441
4yqfGDPSeptin-9/0.441
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.440
1kvkATPMevalonate kinase2.7.1.360.440
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.440
1qorNDPQuinone oxidoreductase 1/0.440
1vikBAYGag-Pol polyprotein/0.440
1yluFMNOxygen-insensitive NAD(P)H nitroreductase/0.440
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2dv3SAHDiphthine synthase/0.440
2rabFADGlutathione amide reductase/0.440
2x0iNAIMalate dehydrogenase/0.440
3hkoANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands/0.440
3mgdACOPredicted acetyltransferase/0.440
4b8wNAPGDP-L-fucose synthase1.1.1.2710.440
4cukNAID-lactate dehydrogenase/0.440
4kx6FADFumarate reductase flavoprotein subunit1.3.5.40.440
4rpgFADUDP-galactopyranose mutase5.4.99.90.440
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.440