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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
4ju11NZGenome polyprotein2.7.7.48

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4ju11NZGenome polyprotein2.7.7.481.000
4ju21O0Genome polyprotein2.7.7.480.676
4jvq1MLGenome polyprotein2.7.7.480.628
4jty1NVGenome polyprotein2.7.7.480.627
4jtw1NUGenome polyprotein2.7.7.480.625
3cj3SX4Genome polyprotein2.7.7.480.588
2girNN3Genome polyprotein2.7.7.480.558
2o5dVR1Genome polyprotein2.7.7.480.554
2d3uCCTPolyprotein/0.533
1nhv154Genome polyprotein2.7.7.480.532
1felFENRetinol-binding protein 4/0.489
1z7yAA5Cysteine synthase 12.5.1.470.487
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.484
1v9aSAHUncharacterized protein/0.478
1q4gBFLProstaglandin G/H synthase 11.14.99.10.474
4pd6URINucleoside permease/0.474
2y05NAPProstaglandin reductase 1/0.473
3ds6A17Mitogen-activated protein kinase 14/0.473
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.473
3wxyCOAUncharacterized protein/0.473
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.472
1sqvUHDCytochrome b/0.471
4cd2FOLDihydrofolate reductase1.5.1.30.471
1ppjANYCytochrome b/0.470
3a7hATPSerine/threonine-protein kinase 242.7.11.10.469
4eqrFADCoenzyme A disulfide reductase/0.468
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.468
4j6bPLOCytochrome P450 monooxygenase/0.467
4j6cSTRCytochrome P450 monooxygenase/0.467
3uhmRFNUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.465
1eqhFLPProstaglandin G/H synthase 11.14.99.10.464
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.464
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.463
1lriCLRBeta-elicitin cryptogein/0.462
2zmd537Dual specificity protein kinase TTK2.7.12.10.461
3h1jSMACytochrome b/0.461
3itzP66Mitogen-activated protein kinase 14/0.461
4o701QKBromodomain-containing protein 4/0.461
2aylFLPProstaglandin G/H synthase 11.14.99.10.460
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.460
3oct1N1Tyrosine-protein kinase BTK2.7.10.20.460
4eevL1XHepatocyte growth factor receptor2.7.10.10.460
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.460
5k2aZMAAdenosine receptor A2a/0.460
1pq944BOxysterols receptor LXR-beta/0.459
1zg32HIIsoflavone 4'-O-methyltransferase/0.459
2hziJINTyrosine-protein kinase ABL12.7.10.20.459
3jynNDPQuinone oxidoreductase/0.459
3tqhNDPQuinone oxidoreductase/0.459
4do30LAFatty-acid amide hydrolase 13.5.1.990.459
1disBDMDihydrofolate reductase1.5.1.30.458
1dkfBMSRetinoic acid receptor alpha/0.458
5ahkTPPAcetolactate synthase II, large subunit/0.458
5k2bZMAAdenosine receptor A2a/0.458
2vbpVB1Isopenicillin N synthase1.21.3.10.457
3vtbTKAVitamin D3 receptor/0.457
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.457
4m9aFDAAcyl-CoA dehydrogenase/0.457
4qa0SHHHistone deacetylase 83.5.1.980.457
5ej8TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.457
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.456
2wo7ASVIsopenicillin N synthase1.21.3.10.456
2ydoADNAdenosine receptor A2a/0.456
3n8wFLPProstaglandin G/H synthase 11.14.99.10.456
4rpgFADUDP-galactopyranose mutase5.4.99.90.456
1aqbRTLRetinol-binding protein 4/0.455
1kt4RTLRetinol-binding protein 4/0.455
1kzjCB3Thymidylate synthase/0.455
2aibERGBeta-elicitin cinnamomin/0.455
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
2oyeIM8Prostaglandin G/H synthase 11.14.99.10.455
4a4wYFBPeroxisome proliferator-activated receptor gamma/0.455
4l9q9TPSerum albumin/0.455
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.455
1rx1NAPDihydrofolate reductase1.5.1.30.454
1yy5FADPolyamine oxidase FMS1/0.454
2aclL05Oxysterols receptor LXR-alpha/0.454
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
3lshFADPyranose 2-oxidase/0.454
3pcfFHBProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.454
4ek816KCyclin-dependent kinase 22.7.11.220.454
4fk8FADFerredoxin--NADP reductase/0.454
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.454
4o4fATPKinase/0.454
5br7FADUDP-galactopyranose mutase/0.454
1kr2TADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.453
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.453
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.453
1wvgAPRCDP-glucose 4,6-dehydratase4.2.1.450.453
1xddAAYIntegrin alpha-L/0.453
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.453
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.453
3cukFADD-amino-acid oxidase1.4.3.30.453
3k6l2BBPeptide deformylase3.5.1.880.453
4qe6JN3Bile acid receptor/0.453
4wujFMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy/0.453
1blzACVIsopenicillin N synthase1.21.3.10.452
1diuBDMDihydrofolate reductase1.5.1.30.452
1rd4L08Integrin alpha-L/0.452
2dw4FADLysine-specific histone demethylase 1A10.452
2q61SF1Peroxisome proliferator-activated receptor gamma/0.452
3bfb9ODPheromone-binding protein ASP1/0.452
3eksCY9Actin-5C/0.452
3kytHC2Nuclear receptor ROR-gamma/0.452
3llkFADSulfhydryl oxidase 11.8.3.20.452
3ntgD72Prostaglandin G/H synthase 21.14.99.10.452
3qlrNDPDihydrofolate reductase1.5.1.30.452
3qlsNDPDihydrofolate reductase1.5.1.30.452
3w8wFADPutative FAD-dependent oxygenase EncM/0.452
5ej7TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.452
1aj8COACitrate synthase/0.451
1qjfACSIsopenicillin N synthase1.21.3.10.451
1tysDHFThymidylate synthase/0.451
2igyA2TPlasmepsin 2/0.451
2xir00JVascular endothelial growth factor receptor 22.7.10.10.451
2ym1FADPhenylacetone monooxygenase1.14.13.920.451
3e8xNAPBH1520 protein/0.451
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.451
3hub469Mitogen-activated protein kinase 14/0.451
3lovFADProtoporphyrinogen oxidase/0.451
3tmz06XCytochrome P450 2B41.14.14.10.451
3wy0COAUncharacterized protein/0.451
4dpmCOAMalonyl-CoA reductase1.2.1.750.451
4l9zCOAL-malyl-CoA/beta-methylmalyl-CoA lyase4.1.3.240.451
4nmdFDABifunctional protein PutA/0.451
5uviZMAAdenosine receptor A2a/0.451
1fbmRTLCartilage oligomeric matrix protein/0.450
1ht834CProstaglandin G/H synthase 11.14.99.10.450
1kt3RTLRetinol-binding protein 4/0.450
1kt7RTLRetinol-binding protein 4/0.450
1wc6TATAdenylate cyclase/0.450
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
2a1uFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.450
3clyACPFibroblast growth factor receptor 2/0.450
3ictCOACoenzyme A disulfide reductase/0.450
3ictADPCoenzyme A disulfide reductase/0.450
4jbtASDCytochrome P450 monooxygenase/0.450
4lxhC1EAlpha/beta hydrolase fold/0.450
1iwjCAMCamphor 5-monooxygenase1.14.15.10.449
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.449
1n4hREANuclear receptor ROR-beta/0.449
1osvCHCBile acid receptor/0.449
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.449
2imkGTXAGAP009194-PA/0.449
2j5xGSPADP-ribosylation factor 6/0.449
3megT27Gag-Pol polyprotein2.7.7.490.449
3nfaCBJGag-Pol polyprotein/0.449
3tk3CPZCytochrome P450 2B41.14.14.10.449
4c4g7RODual specificity protein kinase TTK2.7.12.10.449
4eo80S3Genome polyprotein2.7.7.480.449
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.449
4jbqVX6Aurora kinase A2.7.11.10.449
5fm7ADPRuvB-like helicase/0.449
5i2hAGIO-methyltransferase family 2/0.449
1d7aAIRN5-carboxyaminoimidazole ribonucleotide mutase/0.448
1sr7MOFProgesterone receptor/0.448
1vrqFONSubunit alpha of sarocosine oxidase/0.448
2cciATPCyclin-dependent kinase 22.7.11.220.448
2g78REACellular retinoic acid-binding protein 2/0.448
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
2p33J07Mitogen-activated protein kinase 102.7.11.240.448
3g0eB49Mast/stem cell growth factor receptor Kit2.7.10.10.448
4b4oNDPEpimerase family protein SDR39U1/0.448
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
4dggI76Proto-oncogene tyrosine-protein kinase Src2.7.10.20.448
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.448
5k2dZMAAdenosine receptor A2a/0.448
1errRALEstrogen receptor/0.447
1j3jNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.447
2ydvNECAdenosine receptor A2a/0.447
3i1fGCPTranslation initiation factor 2 subunit gamma/0.447
3mec65BGag-Pol polyprotein2.7.7.490.447
3r5yF42Uncharacterized protein/0.447
4a84DXCMajor pollen allergen Bet v 1-A/0.447
4b1vATPActin, alpha skeletal muscle/0.447
4bb3KKAIsopenicillin N synthase1.21.3.10.447
4klrCHDFerrochelatase, mitochondrial4.99.1.10.447
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.447
5ej6TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.447
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.446
1pmv537Mitogen-activated protein kinase 102.7.11.240.446
1rx7FOLDihydrofolate reductase1.5.1.30.446
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.446
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.446
2qdxFADFerredoxin--NADP+ reductase/0.446
3drcMTXDihydrofolate reductase1.5.1.30.446
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.446
3ijdC2FMethylenetetrahydrofolate reductase/0.446
4ele31IDihydrofolate reductase/0.446
4l2iFADElectron transfer flavoprotein alpha/beta-subunit/0.446
4rrxLURProstaglandin G/H synthase 21.14.99.10.446
1ai9NDPDihydrofolate reductase1.5.1.30.445
2gs7ANPEpidermal growth factor receptor2.7.10.10.445
2r04W71Genome polyprotein/0.445
3dtcVINMitogen-activated protein kinase kinase kinase 92.7.11.250.445
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
3vs6VSHTyrosine-protein kinase HCK2.7.10.20.445
4dc0NDPPutative ketoacyl reductase1.3.10.445
4fdnFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.445
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.445
5iqhGNPBifunctional AAC/APH2.3.10.445
5k2cZMAAdenosine receptor A2a/0.445
1eioGCHGastrotropin/0.444
1hrvSDZGenome polyprotein/0.444
1ia4TQ6Dihydrofolate reductase1.5.1.30.444
1jvsNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.444
1lwlDSOCamphor 5-monooxygenase1.14.15.10.444
2qblCAMCamphor 5-monooxygenase1.14.15.10.444
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3icsADPCoenzyme A disulfide reductase/0.444
3ldfSAHUncharacterized protein/0.444
3pqbVGPPutative oxidoreductase/0.444
3q7dNPXProstaglandin G/H synthase 21.14.99.10.444
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.444
3t88S0N1,4-dihydroxy-2-naphthoyl-CoA synthase/0.444
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4ph9IBPProstaglandin G/H synthase 21.14.99.10.444
5a3bAPRSIR2 family protein/0.444
5dozNDPJamJ/0.444
1jraFADFAD-linked sulfhydryl oxidase ERV21.8.3.20.443
1juvNDPDihydrofolate reductase1.5.1.30.443
1oc1ASVIsopenicillin N synthase1.21.3.10.443
2npnSAMPutative cobalamin synthesis related protein/0.443
2qu6857Vascular endothelial growth factor receptor 22.7.10.10.443
2vcmM11Isopenicillin N synthase1.21.3.10.443
3c3dFO12-phospho-L-lactate transferase/0.443
3h86AP5Adenylate kinase/0.443
3l0lHC3Nuclear receptor ROR-gamma/0.443
4eiyZMAAdenosine receptor A2a/0.443
4f1yCNIGlutamate receptor 3/0.443
4iv21GREstrogen receptor/0.443
4z24FADPutative GMC-type oxidoreductase R13510.443
5iu86DZAdenosine receptor A2a/0.443
1fmjRTLRetinol dehydratase/0.442
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.442
1jpaANPEphrin type-B receptor 22.7.10.10.442
1l3iSAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)/0.442
1xduSFGAclacinomycin 10-hydroxylase RdmB4.1.10.442
2gd2CAAProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.442
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2oj9BMIInsulin-like growth factor 1 receptor2.7.10.10.442
2qa2FADPolyketide oxygenase CabE/0.442
2yiuSMACytochrome b/0.442
2zb1GK4Mitogen-activated protein kinase 14/0.442
3el8PD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.442
3f5p741Insulin-like growth factor 1 receptor2.7.10.10.442
3m0oFADMonomeric sarcosine oxidase1.5.3.10.442
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3pe2E1BCasein kinase II subunit alpha2.7.11.10.442
3vnt0JAVascular endothelial growth factor receptor 22.7.10.10.442
3vs4VSFTyrosine-protein kinase HCK2.7.10.20.442
3wd7COAAcridone synthase/0.442
4ia3BIVVitamin D3 receptor A/0.442
5a3cNADSIR2 family protein/0.442
5bsrCOA4-coumarate--CoA ligase 26.2.1.120.442
5ikrID8Prostaglandin G/H synthase 21.14.99.10.442
5kgpACOPredicted acetyltransferase/0.442
4uhrNGIAdenosine receptor A2a/0.442
1bqoN25Stromelysin-13.4.24.170.441
1brpRTLRetinol-binding protein 4/0.441
1eqgIBPProstaglandin G/H synthase 11.14.99.10.441
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1ot7CHCBile acid receptor/0.441
1u0hONMAdenylate cyclase type 2/0.441
1u0hONMAdenylate cyclase type 5/0.441
1uumAFIDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.441
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.441
3bfa9ODOdorant binding protein ASP1/0.441
3gc9B45Mitogen-activated protein kinase 112.7.11.240.441
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.441
3uwlFOZThymidylate synthase/0.441
3vhkBPKVascular endothelial growth factor receptor 22.7.10.10.441
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.441
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.441
4bdiHAUSerine/threonine-protein kinase Chk22.7.11.10.441
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
4gh5NADShort-chain dehydrogenase/reductase SDR/0.441
4iaq2GM5-hydroxytryptamine receptor 1B/0.441
4j361HRKynurenine 3-monooxygenase/0.441
4ktkKTKCytochrome P450/0.441
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.441
4nr42LKCREB-binding protein/0.441
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.441
5bsfNADPyrroline-5-carboxylate reductase/0.441
5bylGCPBifunctional AAC/APH2.3.10.441
2ycxP32Beta-1 adrenergic receptor/0.441
1ia3TQ5Dihydrofolate reductase1.5.1.30.440
1jedADPSulfate adenylyltransferase/0.440
1nq7ARLNuclear receptor ROR-beta/0.440
1rbqKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.440
1v8kANPKinesin-like protein KIF2C/0.440
1ybgTAVUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
2c475IDCasein kinase I isoform gamma-2/0.440
2ft9CHDFatty acid-binding protein 2, liver/0.440
2vrbNAPTriphenylmethane reductase/0.440
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
3k5uPFQAurora kinase A2.7.11.10.440
3mjrAC2Deoxycytidine kinase2.7.1.740.440
3thrC2FGlycine N-methyltransferase2.1.1.200.440
3v04V04Dual specificity mitogen-activated protein kinase kinase 12.7.12.20.440
3zos0LIEpithelial discoidin domain-containing receptor 12.7.10.10.440
4eqcXR1Serine/threonine-protein kinase PAK 12.7.11.10.440
4id71G0Activated CDC42 kinase 1/0.440
4ktf1TMCytochrome P450/0.440
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.440
4nmbFADBifunctional protein PutA/0.440
5kczNAJAlcohol dehydrogenase E chain1.1.1.10.440
5l7dCLRSmoothened homolog/0.440