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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
4dkv0KWEnvelope glycoprotein gp160

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4dkv0KWEnvelope glycoprotein gp160/1.000
4dku0KUEnvelope glycoprotein gp160/0.588
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.512
4dkp0LLEnvelope glycoprotein gp160/0.503
2bxmIMNSerum albumin/0.498
4c717RD3-oxoacyl-ACP synthase/0.497
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.496
5dp2NAPCurF/0.493
4dvv0M1Envelope glycoprotein gp160/0.492
1opbRETRetinol-binding protein 2/0.490
4c72TLG3-oxoacyl-ACP synthase/0.490
4dko0LMEnvelope glycoprotein gp160/0.489
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.488
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.486
4jv3N32Beta-ketoacyl synthase/0.486
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.485
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.484
3oafOAGDihydrofolate reductase1.5.1.30.483
2aqbTL63-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.481
3qlrNDPDihydrofolate reductase1.5.1.30.478
5a27MYAGlycylpeptide N-tetradecanoyltransferase/0.478
5dozNDPJamJ/0.477
4brdANPEctonucleoside triphosphate diphosphohydrolase I/0.474
2wgeTLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.473
4qzuRTLRetinol-binding protein 2/0.473
1p0pBCHCholinesterase3.1.1.80.472
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.472
4qvtACOAcetyltransferase YpeA2.3.10.472
1bk0ACVIsopenicillin N synthase1.21.3.10.470
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
4b13NHWGlycylpeptide N-tetradecanoyltransferase/0.470
4bfsZVSPantothenate kinase2.7.1.330.470
4bfxZVXPantothenate kinase2.7.1.330.470
1zrzBI1Protein kinase C iota type2.7.11.130.469
3mtfA3FActivin receptor type-12.7.11.300.469
4rquNADAlcohol dehydrogenase class-P/0.468
2bdyUNBProthrombin3.4.21.50.467
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
2jdtI5ScAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.467
3af2ACPPantothenate kinase2.7.1.330.466
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.466
1osvCHCBile acid receptor/0.465
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.465
3ukuC69Actin-related protein 3/0.465
4q71FADBifunctional protein PutA/0.465
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.464
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.463
1tduDURThymidylate synthase/0.463
1w06W05Isopenicillin N synthase1.21.3.10.463
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.463
2g8yNADHydroxycarboxylate dehydrogenase B/0.463
3h3t16HCollagen type IV alpha-3-binding protein/0.463
1yc2NADNAD-dependent protein deacylase 2/0.462
4bftZVTPantothenate kinase2.7.1.330.462
4qofFMNRibosyldihydronicotinamide dehydrogenase [quinone]/0.462
2b4yAPRNAD-dependent protein deacylase sirtuin-5, mitochondrial/0.461
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.461
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.461
4in44IDKelch-like ECH-associated protein 1/0.461
1gveNAPAflatoxin B1 aldehyde reductase member 310.460
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
3vspEK8Peroxisome proliferator-activated receptor gamma/0.460
3zkyWT4Isopenicillin N synthase1.21.3.10.460
4jtqNAPAldo-keto reductase family 1 member C2/0.460
5cp8TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
2cvjFADThioredoxin reductase related protein/0.459
2ftoCB3Thymidylate synthase/0.459
2kceD16Thymidylate synthase/0.459
2lfoGCHFatty acid-binding protein, liver/0.459
3fr0AJBGlucokinase2.7.1.20.459
3vy5FMNFMN-binding protein/0.459
4c73TLH3-oxoacyl-ACP synthase/0.459
4i531C1Envelope glycoprotein gp160/0.459
5fm7ADPRuvB-like helicase/0.459
2jh5895Prothrombin3.4.21.50.458
2nr4FMNConserved protein/0.458
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.458
3own3OWRenin3.4.23.150.458
4q72FADBifunctional protein PutA/0.458
1a5bIGPTryptophan synthase alpha chain/0.457
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.457
1x2hLPALipoate-protein ligase A6.3.1.200.457
2rqfJH3Hemolymph juvenile hormone binding protein/0.457
2xvv9DNSerum albumin/0.457
2zhf49UProthrombin3.4.21.50.457
3e8xNAPBH1520 protein/0.457
3r83Z14Cyclin-dependent kinase 22.7.11.220.457
4bfvZVVPantothenate kinase2.7.1.330.457
1c4vIH2Prothrombin3.4.21.50.456
1fmjRTLRetinol dehydratase/0.456
1hb1OCVIsopenicillin N synthase1.21.3.10.456
1o2g696Prothrombin3.4.21.50.456
3cukFADD-amino-acid oxidase1.4.3.30.456
3pqbVGPPutative oxidoreductase/0.456
3saz043Malate synthase G/0.456
3znqSS8D-amino-acid oxidase1.4.3.30.456
4a81DXCMajor pollen allergen Bet v 1-A/0.456
5e7oMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.456
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
1mczTDPBenzoylformate decarboxylase4.1.1.70.455
1qorNDPQuinone oxidoreductase 1/0.455
2gv8NDPThiol-specific monooxygenase1.14.130.455
3g11P9C3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.455
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.455
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.455
3sn6P0GBeta-2 adrenergic receptor/0.455
1cjkFOKAdenylate cyclase type 2/0.454
1cjkFOKAdenylate cyclase type 5/0.454
1drhNAPDihydrofolate reductase1.5.1.30.454
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
3ho2N323-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.454
3id8MRKGlucokinase2.7.1.20.454
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
2zevB71Geranylgeranyl pyrophosphate synthase/0.453
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
4hs4FMNChromate reductase/0.453
4jbtASDCytochrome P450 monooxygenase/0.453
1a72PADAlcohol dehydrogenase E chain1.1.1.10.452
1kceCB3Thymidylate synthase/0.452
2dhfDZFDihydrofolate reductase1.5.1.30.452
2gvdFKPAdenylate cyclase type 2/0.452
2gvdFKPAdenylate cyclase type 5/0.452
2xlrNAPPutative flavin-containing monooxygenase/0.452
2zgb21UProthrombin3.4.21.50.452
2zhq27UProthrombin3.4.21.50.452
3qrwNDPPutative ketoacyl reductase1.3.10.452
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.452
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
5ag5MYAGlycylpeptide N-tetradecanoyltransferase/0.452
1d3dBZTProthrombin3.4.21.50.451
1fmlRTLRetinol dehydratase/0.451
3c6n2S8Protein TRANSPORT INHIBITOR RESPONSE 1/0.451
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.451
1d6w00RProthrombin3.4.21.50.450
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.450
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.450
4dc0NDPPutative ketoacyl reductase1.3.10.450
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.450
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.450
4l4xNDPAmphI/0.450
1crbRTLRetinol-binding protein 1/0.449
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1fndA2PFerredoxin--NADP reductase, chloroplastic1.18.1.20.449
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.449
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.449
2bunFADAppA protein/0.449
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.449
2gevCOKPantothenate kinase2.7.1.330.449
3hub469Mitogen-activated protein kinase 14/0.449
4bgg844Activin receptor type-12.7.11.300.449
4dymIYZActivin receptor type-12.7.11.300.449
4twnB96Ephrin type-A receptor 32.7.10.10.449
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.449
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.448
1kvkATPMevalonate kinase2.7.1.360.448
1mczRMNBenzoylformate decarboxylase4.1.1.70.448
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.448
1ppjANYCytochrome b/0.448
1qoqIGPTryptophan synthase alpha chain/0.448
1u1iNADMyo-inositol-1-phosphate synthase (Ino1)/0.448
4c6uTLG3-oxoacyl-ACP synthase/0.448
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.448
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.447
3br3ETHTH-type transcriptional regulator QacR/0.447
4fam0SZAldo-keto reductase family 1 member C3/0.447
5c7hNDPPutative oxidoreductase/0.447
1rx8NAPDihydrofolate reductase1.5.1.30.446
1v4sMRKGlucokinase2.7.1.20.446
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
2h94FADLysine-specific histone demethylase 1A10.446
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.446
2x7hPFNProstaglandin reductase 310.446
2xs4ALA_PHE_THRKarilysin3.4.240.446
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4er6AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.446
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.446
4pmjNAPPutative oxidoreductase/0.446
4xq9NADHomospermidine synthase2.5.1.440.446
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3b9lAZZSerum albumin/0.445
3bk2U5PRibonuclease J/0.445
4dc1NDPPutative ketoacyl reductase1.3.10.445
4lb2DM5Serum albumin/0.445
1b2lNDCAlcohol dehydrogenase1.1.1.10.444
1kqwRTLCellular retinol-binding protein type II/0.444
1oc1ASVIsopenicillin N synthase1.21.3.10.444
2q5qTPWIndole-3-pyruvate decarboxylase4.1.1.740.444
2rg5279Mitogen-activated protein kinase 14/0.444
2ykeYKEHeat shock protein HSP 90-alpha/0.444
3e92G6AMitogen-activated protein kinase 14/0.444
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.444
3uleC69Actin-related protein 3/0.444
4ceqQCHIntegrase/0.444
4ck2NVUIntegrase/0.444
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.444
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.444
4g95OAGDihydrofolate reductase1.5.1.30.444
4kin1M8Mitogen-activated protein kinase 14/0.444
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
4ea30NNNociceptin receptor/0.444
1g69TZPThiamine-phosphate synthase/0.443
1mvsDTMDihydrofolate reductase1.5.1.30.443
1n83CLRNuclear receptor ROR-alpha/0.443
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
2rbeZMGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
2rgoFADAlpha-Glycerophosphate Oxidase/0.443
2wo7ASVIsopenicillin N synthase1.21.3.10.443
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
2ycnP61Tyrosine phenol-lyase4.1.99.20.443
3bl7DD1m7GpppX diphosphatase3.6.1.590.443
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.443
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.443
3ibdCPZCytochrome P450 2B61.14.130.443
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3phjDHKShikimate dehydrogenase (NADP(+))/0.443
3qwbNDPProbable quinone oxidoreductase1.6.5.50.443
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.443
4g67SAHUncharacterized ACR, COG1565 superfamily/0.443
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.443
4i4b1CV3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.443
1v35NAIEnoyl-ACP reductase/0.442
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
1zc3GNPRas-related protein Ral-A/0.442
2oj9BMIInsulin-like growth factor 1 receptor2.7.10.10.442
3anmNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.442
4e5yNDPGDP-L-fucose synthase1.1.1.2710.442
4imfSI3N-acetylneuraminate lyase/0.442
4ks7X4ZSerine/threonine-protein kinase PAK 62.7.11.10.442
4yxsEMUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
1dyiFOLDihydrofolate reductase1.5.1.30.441
1fwkADPHomoserine kinase2.7.1.390.441
1fwyUD1Bifunctional protein GlmU/0.441
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.441
1r6g442Thyroid hormone receptor beta/0.441
1ypkCCRProthrombin3.4.21.50.441
2bacFADPutative aminooxidase/0.441
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.441
2iviACWIsopenicillin N synthase1.21.3.10.441
2nmtNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.441
2vqbNAPPutative flavin-containing monooxygenase/0.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3hucG97Mitogen-activated protein kinase 14/0.441
3nj0PYVAbscisic acid receptor PYL2/0.441
3zh8C58Protein kinase C iota type2.7.11.130.441
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.441
4j3mAJ8Tankyrase-22.4.2.300.441
4m6jNDPDihydrofolate reductase1.5.1.30.441
4z87GDPInosine-5'-monophosphate dehydrogenase/0.441
5ero210Fusicoccadiene synthase2.5.1.290.441
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.441
5hynSAHHistone-lysine N-methyltransferase EZH22.1.1.430.441
3qakUKAAdenosine receptor A2a/0.441
1afeALZProthrombin3.4.21.50.440
1uycPU7Heat shock protein HSP 90-alpha/0.440
1wsvTHHAminomethyltransferase, mitochondrial/0.440
2bn4FADNADPH--cytochrome P450 reductase/0.440
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.440
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.440
2xh9J01Uncharacterized protein/0.440
3aosJH2Hemolymph juvenile hormone binding protein/0.440
3dufR1TPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.440
3dufR1TPyruvate dehydrogenase E1 component subunit beta1.2.4.10.440
3juqAJDPhenazine biosynthesis protein A/B/0.440
3t37FADPyridoxine 4-oxidase/0.440
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.440
4a86H35Major pollen allergen Bet v 1-A/0.440
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.440
4c02TAKActivin receptor type-12.7.11.300.440
4i6gFADCryptochrome-2/0.440
4nmdFDABifunctional protein PutA/0.440
5kgjACOPredicted acetyltransferase/0.440