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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
2eckADPAdenylate kinase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2eckADPAdenylate kinase/1.000
1akeAP5Adenylate kinase/0.755
4x8oAP5Adenylate kinase/0.606
4qbiAP5Adenylate kinase/0.597
1p3jAP5Adenylate kinase/0.586
3hpqAP5Adenylate kinase/0.586
2oo7AP5Adenylate kinase/0.585
3dkvAP5Adenylate kinase/0.584
2eu8AP5Adenylate kinase/0.574
4qbhAP5Adenylate kinase/0.573
4nu0AP5Adenylate kinase/0.565
4jl5ADPAdenylate kinase/0.563
1ankANPAdenylate kinase/0.562
4x8lAP5Adenylate kinase/0.554
4cf7ADPAdenylate kinase/0.553
2rgxAP5Adenylate kinase/0.546
4jl6ADPAdenylate kinase/0.541
2akyAP5Adenylate kinase/0.537
4jkyADPAdenylate kinase/0.511
2x0rNADMalate dehydrogenase/0.504
3s79ASDAromatase1.14.14.140.495
4f6w0SSCyclin-dependent kinase 82.7.11.220.492
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.490
2bunFADAppA protein/0.487
1d7aAIRN5-carboxyaminoimidazole ribonucleotide mutase/0.477
3ed1GA3Gibberellin receptor GID1/0.477
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.476
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.476
3stxBKAMethylketone synthase I/0.476
2q6bHR23-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.475
3m2rCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.475
3m2rCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.475
1g9cBABBotulinum neurotoxin type B3.4.24.690.473
2daaDCSD-alanine aminotransferase2.6.1.210.473
1h51FMNPentaerythritol tetranitrate reductase/0.472
2q5oTPWIndole-3-pyruvate decarboxylase4.1.1.740.472
4zohFADPutative oxidoreductase FAD-binding subunit/0.472
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.471
3crlANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.470
3fgoACPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.470
3v49PK0Androgen receptor/0.470
4loh1SYStimulator of interferon genes protein/0.470
2rkvZBATrichothecene 3-O-acetyltransferase/0.469
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
4n49MGTCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 12.1.1.570.468
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.467
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.467
2od7A1RNAD-dependent protein deacetylase HST23.5.10.466
3elm24FCollagenase 33.4.240.466
3fql79ZGenome polyprotein2.7.7.480.466
4appN53Serine/threonine-protein kinase PAK 42.7.11.10.466
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.465
2q5oPPYIndole-3-pyruvate decarboxylase4.1.1.740.465
3gg0FMNUncharacterized protein/0.465
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.465
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.464
2x7hPFNProstaglandin reductase 310.464
3pvwQRXBeta-adrenergic receptor kinase 12.7.11.150.464
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
1a59COA2-methylcitrate synthase/0.462
3cppCAMCamphor 5-monooxygenase1.14.15.10.462
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.462
4loi1YCStimulator of interferon genes protein/0.462
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.461
2zshGA3Gibberellin receptor GID1A30.461
3a62STURibosomal protein S6 kinase beta-12.7.11.10.461
4ai8DZAHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.461
5kgpACOPredicted acetyltransferase/0.461
1g0rTHMGlucose-1-phosphate thymidylyltransferase/0.460
1sxjADPReplication factor C subunit 5/0.460
4e5kNADPhosphonate dehydrogenase1.20.1.10.460
4i6gFADCryptochrome-2/0.460
4u7wNDPMxaA/0.460
5kghACOPredicted acetyltransferase/0.460
1cs4FOKAdenylate cyclase type 2/0.459
1cs4FOKAdenylate cyclase type 5/0.459
1f9aATPNicotinamide-nucleotide adenylyltransferase/0.459
1ybaNADD-3-phosphoglycerate dehydrogenase1.1.1.950.459
2iyiFMNAppA, antirepressor of ppsR, sensor of blue light/0.459
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.459
1g4pFQPThiamine-phosphate synthase/0.458
2jlbUDMUncharacterized protein/0.458
3otwCOAPhosphopantetheine adenylyltransferase/0.458
3p62FMNPentaerythritol tetranitrate reductase/0.458
4u0mGTPCyclic GMP-AMP synthase/0.458
1j7kATPHolliday junction ATP-dependent DNA helicase RuvB/0.457
3gcq1BUMitogen-activated protein kinase 14/0.457
3nbzGTPGTP-binding nuclear protein Ran/0.457
4lgaA2OAbscisic acid receptor PYL2/0.457
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.456
1lhwESMSex hormone-binding globulin/0.456
2gmvPEPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.456
3cd57HI3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.456
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.456
3wb2YGPUncharacterized protein MJ0488/0.456
4dpwAGSMevalonate diphosphate decarboxylase/0.456
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.455
4bewACPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.455
4gk3L87Ephrin type-A receptor 32.7.10.10.455
1mezGDPAdenylosuccinate synthetase isozyme 1/0.454
2bpoNAPNADPH--cytochrome P450 reductase/0.454
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
3fp0FP015-O-acetyltransferase/0.454
3p23ADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.454
3p97SAMGenome polyprotein2.1.1.560.454
3qgtCP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.454
3qlrNDPDihydrofolate reductase1.5.1.30.454
4asyN5YGlucose-1-phosphate thymidylyltransferase/0.454
4e2bFMNDehydrogenase/0.454
4x30T44Thyroxine-binding globulin/0.454
1ja1NAPNADPH--cytochrome P450 reductase/0.453
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
2xpwOTCTetracycline repressor protein class D/0.453
3cgdCOACoenzyme A disulfide reductase/0.453
3eblGA4Gibberellin receptor GID1/0.453
3nxoD2BDihydrofolate reductase1.5.1.30.453
4bb432WEphrin type-B receptor 42.7.10.10.453
4kin1M8Mitogen-activated protein kinase 14/0.453
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.453
4yswFADXanthine dehydrogenase/oxidase/0.453
5kf1ACOPredicted acetyltransferase/0.453
1g4tFTPThiamine-phosphate synthase/0.452
1w78PD8Dihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.452
3h4vDVPPteridine reductase 11.5.1.330.452
3to3ATPPetrobactin biosynthesis protein AsbB/0.452
4dp3MMVBifunctional dihydrofolate reductase-thymidylate synthase/0.452
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.452
5kgjACOPredicted acetyltransferase/0.452
2eklNADD-3-phosphoglycerate dehydrogenase/0.451
3c14FOKAdenylate cyclase type 2/0.451
3c14FOKAdenylate cyclase type 5/0.451
3ibqATPPyridoxal kinase/0.451
4a7b3W5Collagenase 33.4.240.451
4e37NDPCatalase1.11.1.60.451
4l9q9TPSerum albumin/0.451
4r1lADPPhenylacetate-coenzyme A ligase/0.451
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.451
1bifAGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 42.7.1.1050.450
1p4aPCPPur operon repressor/0.450
1ykdCMPAdenylate cyclase/0.450
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.450
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2j08FADDeoxyribodipyrimidine photo-lyase4.1.99.30.450
2rg6287Mitogen-activated protein kinase 14/0.450
2y3rTIRTamL/0.450
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
2zsiGA4Gibberellin receptor GID1A30.450
3bazNAPHydroxyphenylpyruvate reductase1.1.1.2370.450
3mgdACOPredicted acetyltransferase/0.450
3mjhGTPRas-related protein Rab-5A/0.450
3nmpPYVAbscisic acid receptor PYL2/0.450
3qiyQI1Botulinum neurotoxin type A3.4.24.690.450
4gk2L66Ephrin type-A receptor 32.7.10.10.450
4h2nFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.450
4nvk2NYPeroxidase/0.450
4xyeNADFormate dehydrogenase/0.450
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.449
2vprTDCTetracycline repressor protein class H/0.449
2yxuATPPyridoxal kinase2.7.1.350.449
3gluLYS_VAL_METNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.449
3oibFDAPutative acyl-CoA dehydrogenase/0.449
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
4fsrHKCSerine/threonine-protein kinase Chk12.7.11.10.449
4ma628EAra h 8 allergen/0.449
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.449
5kf9ACOPredicted acetyltransferase/0.449
1os1ATPPhosphoenolpyruvate carboxykinase (ATP)/0.448
1q43CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2/0.448
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
2p2xSAHDiphthine synthase/0.448
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.448
4u0oMTALipoyl synthase 2/0.448
4v02ATPSite-determining protein/0.448
4wqmFADToluene-4-monooxygenase electron transfer component1.18.1.30.448
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.448
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
1nzdUPGDNA beta-glucosyltransferase/0.447
2bueCOAAAC(6')-Ib/0.447
2przOMPOrotate phosphoribosyltransferase 12.4.2.100.447
3k145352-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.447
3qfxCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
4d0lGSPRas-related protein Rab-11A/0.447
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.447
4nt03DUOrotidine 5'-phosphate decarboxylase4.1.1.230.447
4oznATPAmmonium transporter/0.447
4yerADPAntibiotic ABC transporter, ATP-binding protein, putative/0.447
5aluHD2Bifunctional epoxide hydrolase 23.1.3.760.447
5cnsCDPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.447
5dp2NAPCurF/0.447
1dkfBMSRetinoic acid receptor alpha/0.446
1g67TZPThiamine-phosphate synthase/0.446
1hdrNADDihydropteridine reductase1.5.1.340.446
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.446
2cahNDPCatalase1.11.1.60.446
2iypA2P6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.446
2o12FMNChorismate synthase/0.446
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.446
2qocANPEphrin type-A receptor 32.7.10.10.446
3cbsR12Cellular retinoic acid-binding protein 2/0.446
3oiaA31Camphor 5-monooxygenase1.14.15.10.446
3r2b05BMAP kinase-activated protein kinase 22.7.11.10.446
3t3iGPWGlycogen phosphorylase, muscle form2.4.1.10.446
4c717RD3-oxoacyl-ACP synthase/0.446
4e09ACPPlasmid partitioning protein ParF/0.446
4jb1FADUDP-N-acetylenolpyruvoylglucosamine reductase/0.446
4jxxATPGlutamine--tRNA ligase6.1.1.180.446
4twnB96Ephrin type-A receptor 32.7.10.10.446
5kf8ACOPredicted acetyltransferase/0.446
1culFOKAdenylate cyclase type 2/0.445
1culFOKAdenylate cyclase type 5/0.445
1hvyD16Thymidylate synthase2.1.1.450.445
1kqfMGDFormate dehydrogenase, nitrate-inducible, major subunit1.1.5.60.445
1s4eADPGalactokinase/0.445
1z45UPGBifunctional protein GAL105.1.3.20.445
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.445
2hr8SAHDiphthine synthase/0.445
2p5uNADUDP-glucose 4-epimerase/0.445
2y6o1N1Ephrin type-A receptor 42.7.10.10.445
3iphG11Mitogen-activated protein kinase 14/0.445
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.445
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.445
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.445
4kiq1RAMitogen-activated protein kinase 14/0.445
4qaiFMNNADPH dehydrogenase/0.445
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.445
1esvLARActin, alpha skeletal muscle/0.444
1gjrNAPFerredoxin--NADP reductase1.18.1.20.444
1tllNAPNitric oxide synthase, brain1.14.13.390.444
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.444
2acxANPG protein-coupled receptor kinase 62.7.11.160.444
2v5aLZLBiotin carboxylase6.3.4.140.444
2zm1KSFTyrosine-protein kinase Lck2.7.10.20.444
3f3sNADLambda-crystallin homolog/0.444
3k2hLYABifunctional dihydrofolate reductase-thymidylate synthase/0.444
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.444
4lb2DM5Serum albumin/0.444
4uyg73BBromodomain-containing protein 2/0.444
4wjiNAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase/0.444
1hlk113Metallo-beta-lactamase type 2/0.443
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.443
1w7iADPUnconventional myosin-Va/0.443
1xelUPGUDP-glucose 4-epimerase5.1.3.20.443
1yjqNAP2-dehydropantoate 2-reductase1.1.1.1690.443
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.443
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.443
2gmjFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.443
2vbpVB1Isopenicillin N synthase1.21.3.10.443
3c6n2S8Protein TRANSPORT INHIBITOR RESPONSE 1/0.443
3gbuATPUncharacterized sugar kinase PH14592.7.10.443
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.443
3owj1ELCasein kinase II subunit alpha2.7.11.10.443
3qfcNAPNADPH--cytochrome P450 reductase/0.443
3vi7CBDHematopoietic prostaglandin D synthase/0.443
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4rjeFNRLactate oxidase/0.443
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.442
2bu8ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.442
2w8rADPSuccinate-semialdehyde dehydrogenase, mitochondrial1.2.1.240.442
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.442
3tydXHPDihydropteroate synthase/0.442
3x2vATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
3zeiAWHO-acetylserine sulfhydrylase/0.442
4d7eFADPutative lysine-N-oxygenase/0.442
4fv3EK6Mitogen-activated protein kinase 12.7.11.240.442
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
4weqNAPNAD-dependent dehydrogenase/0.442
4yl2FMNLactate oxidase/0.442
5dacAGSUncharacterized protein/0.442
1bwkFMNNADPH dehydrogenase 11.6.99.10.441
1cqp803Integrin alpha-L/0.441
1dliUDXUDP-glucose 6-dehydrogenase/0.441
1kl2FONSerine hydroxymethyltransferase/0.441
1pd9CO4Dihydrofolate reductase1.5.1.30.441
1pn3TYDdTDP-epi-vancosaminyltransferase2.4.1.3110.441
2dwpACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.441
2o1vADPEndoplasmin/0.441
2ym2FADPhenylacetone monooxygenase1.14.13.920.441
3fr4F8AFatty acid-binding protein, adipocyte/0.441
3hyg099A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.441
3maaFKPAdenylate cyclase type 2/0.441
3maaFKPAdenylate cyclase type 5/0.441
3q95ESLEstrogen receptor/0.441
3ssmSAHMycinamicin VI 2''-O-methyltransferase/0.441
3vv8B02Beta-secretase 13.4.23.460.441
4ansVGHALK tyrosine kinase receptor2.7.10.10.441
4emjFADToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component1.18.1.30.441
4eutBX7Serine/threonine-protein kinase TBK12.7.11.10.441
4nh0ATPESX secretion system protein EccC/0.441
5aacVGHALK tyrosine kinase receptor2.7.10.10.441
1d4dFADFumarate reductase flavoprotein subunit1.3.5.40.440
1f20NAPNitric oxide synthase, brain1.14.13.390.440
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.440
1i2lDCSAminodeoxychorismate lyase4.1.3.380.440
1lwlDSOCamphor 5-monooxygenase1.14.15.10.440
1m8gNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.440
1r2jFADFkbI/0.440
1toiHCIAspartate aminotransferase2.6.1.10.440
1vcfFMNIsopentenyl-diphosphate delta-isomerase/0.440
1wpgADPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.440
1y8qATPSUMO-activating enzyme subunit 26.3.20.440
2npxNADNADH peroxidase1.11.1.10.440
2uyyNA7Putative oxidoreductase GLYR110.440
2vd0D27Hematopoietic prostaglandin D synthase/0.440
2xvv9DNSerum albumin/0.440
2z6rSAHDiphthine synthase/0.440
3evaSAHGenome polyprotein2.1.1.560.440
3frqERYErythromycin resistance repressor protein/0.440
3gfyFMNUncharacterized protein/0.440
3i2834NBifunctional epoxide hydrolase 23.3.2.100.440
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
3qe2NAPNADPH--cytochrome P450 reductase/0.440
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
4ajj88RL-lactate dehydrogenase A chain1.1.1.270.440
4h4qFADBiphenyl dioxygenase ferredoxin reductase subunit/0.440
4iadADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
4kh0ATPAspartate carbamoyltransferase regulatory chain {ECO:0000256|HAMAP-Rule:MF_00002}/0.440
4lhvGDPRas-related protein Rab-8A/0.440
4pl3ADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.440
4riyADPEpidermal growth factor receptor2.7.10.10.440