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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
1yslCOAHydroxymethylglutaryl-CoA synthase2.3.3.10

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1yslCOAHydroxymethylglutaryl-CoA synthase2.3.3.101.000
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.612
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.601
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.599
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.591
1txtCAAHMG-CoA synthase/0.587
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.567
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.556
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.546
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.534
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.509
2vcmM11Isopenicillin N synthase1.21.3.10.502
4c49HCYCorticosteroid-binding globulin/0.496
1toiHCIAspartate aminotransferase2.6.1.10.493
2pg0FADAcyl-CoA dehydrogenase/0.491
1osvCHCBile acid receptor/0.490
2ibwCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.490
2wo7ASVIsopenicillin N synthase1.21.3.10.490
4oztP1AEcdysone receptor, putative/0.490
4dvi2IWTankyrase-12.4.2.300.487
3zkyWT4Isopenicillin N synthase1.21.3.10.485
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.479
4twnB96Ephrin type-A receptor 32.7.10.10.478
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.477
2ibyCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.477
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.477
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.474
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.474
1ez0NAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.473
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.473
3q9bB3NAcetylpolyamine amidohydrolase/0.473
2v59LZKBiotin carboxylase6.3.4.140.472
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.472
1qsnCOAHAT A1/0.471
2bxmIMNSerum albumin/0.471
4qzuRTLRetinol-binding protein 2/0.471
2vbpVB1Isopenicillin N synthase1.21.3.10.470
4r1lADPPhenylacetate-coenzyme A ligase/0.470
4a862ANMajor pollen allergen Bet v 1-A/0.469
4ubtCOASteroid 3-ketoacyl-CoA thiolase/0.469
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.468
1d3dBZTProthrombin3.4.21.50.467
1kvkATPMevalonate kinase2.7.1.360.467
1lf3EH5Plasmepsin-23.4.23.390.467
1qiqACCIsopenicillin N synthase1.21.3.10.467
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.467
3qiyQI1Botulinum neurotoxin type A3.4.24.690.467
1bk0ACVIsopenicillin N synthase1.21.3.10.466
1blzACVIsopenicillin N synthase1.21.3.10.466
1trkTPPTransketolase 12.2.1.10.466
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
1d3pBT3Prothrombin3.4.21.50.465
3fhxPLPPyridoxal kinase2.7.1.350.465
4c6uTLG3-oxoacyl-ACP synthase/0.465
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.465
4h6uACOAlpha-tubulin N-acetyltransferase 1/0.465
1kceCB3Thymidylate synthase/0.464
2w6zL21Biotin carboxylase6.3.4.140.464
3eksCY9Actin-5C/0.464
3nx2FERFerulic acid decarboxylase/0.464
3rk507ZCyclin-dependent kinase 22.7.11.220.464
4qe6JN3Bile acid receptor/0.464
2rhrEMOPutative ketoacyl reductase1.3.10.463
4ddrMMVDihydrofolate reductase1.5.1.30.463
1kqfMGDFormate dehydrogenase, nitrate-inducible, major subunit1.1.5.60.462
2f2sCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.462
3hwxTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.462
4bb3KKAIsopenicillin N synthase1.21.3.10.462
5cb3APRO-acetyl-ADP-ribose deacetylase/0.462
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.461
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1qoqIGPTryptophan synthase alpha chain/0.461
2a9z26AAdenosine kinase2.7.1.200.461
3dufR1TPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.461
3dufR1TPyruvate dehydrogenase E1 component subunit beta1.2.4.10.461
3h3r14HCollagen type IV alpha-3-binding protein/0.461
4jq3NAPAldo-keto reductase family 1 member C2/0.461
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.460
2w06FRVCyclin-dependent kinase 22.7.11.220.460
4h6zACOAlpha-tubulin N-acetyltransferase 1/0.460
4zm6ACON-acetyl-beta-D glucosaminidase/0.460
5kf9ACOPredicted acetyltransferase/0.460
1pu9COAHAT A1/0.459
3rix923Luciferin 4-monooxygenase1.13.12.70.459
5kf8ACOPredicted acetyltransferase/0.459
1qjfACSIsopenicillin N synthase1.21.3.10.458
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.458
3ful52DLeukotriene A-4 hydrolase3.3.2.60.458
3qwc98PProthrombin3.4.21.50.458
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.458
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.458
5epoTUD7-alpha-hydroxysteroid deydrogenase/0.458
1h50FMNPentaerythritol tetranitrate reductase/0.457
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.457
1rx8NAPDihydrofolate reductase1.5.1.30.457
1zgv501Prothrombin3.4.21.50.457
2g78REACellular retinoic acid-binding protein 2/0.457
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.457
5idwNAPShort-chain dehydrogenase/reductase SDR/0.457
1kqwRTLCellular retinol-binding protein type II/0.456
1qy5NECEndoplasmin/0.456
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.456
1stdBFSScytalone dehydratase4.2.1.940.456
2pdaTPPPyruvate synthase/0.456
2wgeTLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.456
3up0D7SaceDAF-12/0.456
1obnASVIsopenicillin N synthase1.21.3.10.455
1pq944BOxysterols receptor LXR-beta/0.455
1xagNAD3-dehydroquinate synthase/0.455
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
2bu9HFVIsopenicillin N synthase1.21.3.10.455
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.455
2xhrC0PHeat shock protein HSP 90-alpha/0.455
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.455
3fp0FP015-O-acetyltransferase/0.455
3rq8AP5ADP-dependent (S)-NAD(P)H-hydrate dehydratase/0.455
3tjsD0RCytochrome P450 3A4/0.455
4eh8IRGMitogen-activated protein kinase 14/0.455
4ku5DCC3-oxoacyl-[ACP] synthase III/0.455
4yjdFADD-amino-acid oxidase1.4.3.30.455
4zthGG5Mitogen-activated protein kinase 14/0.455
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
1sdmADPKinesin heavy chain-like protein/0.454
2bxqIMNSerum albumin/0.454
2pswCOAN-alpha-acetyltransferase 50/0.454
4jqlVJ6Heat shock protein HSP 90-alpha/0.454
4rvnCOAPhenylacetate-coenzyme A ligase/0.454
1f5fDHTSex hormone-binding globulin/0.453
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
1hfqMOTDihydrofolate reductase1.5.1.30.453
1me6IVSPlasmepsin-23.4.23.390.453
1mrqSTRAldo-keto reductase family 1 member C1/0.453
1q3hANPCystic fibrosis transmembrane conductance regulator/0.453
1trgCB3Thymidylate synthase/0.453
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.453
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.453
3h3t16HCollagen type IV alpha-3-binding protein/0.453
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.453
2b1z17MEstrogen receptor/0.452
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.452
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.452
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.452
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.452
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.452
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.452
4fcr0TMHeat shock protein HSP 90-alpha/0.452
1x8lOXRRetinol dehydratase/0.451
2e08SAHDiphthine synthase/0.451
3djfBC3Purine nucleoside phosphorylase/0.451
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
3ghwGHWDihydrofolate reductase1.5.1.30.451
4bfxZVXPantothenate kinase2.7.1.330.451
4dptAGSMevalonate diphosphate decarboxylase/0.451
4fdnFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.451
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4i02CMPcAMP-activated global transcriptional regulator CRP/0.451
2bgsNDPAldose reductase1.1.1.210.450
2e17SAHDiphthine synthase/0.450
2fhnBNIAvidin-related protein 4/5/0.450
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.450
2iviACWIsopenicillin N synthase1.21.3.10.450
2pvjP44Casein kinase II subunit alpha2.7.11.10.450
3c3xNAPEugenol synthase 11.1.1.3180.450
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.450
4bfvZVVPantothenate kinase2.7.1.330.450
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.449
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.449
1lnmDTXBilin-binding protein/0.449
1t4v14AProthrombin3.4.21.50.449
2bf7HBIPteridine reductase 11.5.1.330.449
2bunFADAppA protein/0.449
2fxuBIDActin, alpha skeletal muscle/0.449
2plmSIB5-methylthioadenosine/S-adenosylhomocysteine deaminase3.5.4.280.449
3bwjARXcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.449
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.449
3uxvGUNNADPH-dependent 7-cyano-7-deazaguanine reductase/0.449
4an4DUDPutative glycosyl transferase/0.449
4iarERM5-hydroxytryptamine receptor 1B/0.449
4uyf73BBromodomain-containing protein 2/0.449
1x2hLPALipoate-protein ligase A6.3.1.200.448
2cy2ACOProbable acetyltransferase/0.448
2g0gSP0Peroxisome proliferator-activated receptor gamma/0.448
2jibADPOxalyl-CoA decarboxylase4.1.1.80.448
2op18PCEnoyl-ACP reductase/0.448
3fpjSAMUncharacterized protein/0.448
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.448
4bftZVTPantothenate kinase2.7.1.330.448
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.448
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.448
4mqt2CUMuscarinic acetylcholine receptor M2/0.448
3sn6P0GBeta-2 adrenergic receptor/0.448
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.447
1ofgNDPGlucose--fructose oxidoreductase1.1.99.280.447
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.447
1t7o152Carnitine O-acetyltransferase2.3.1.70.447
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
3gwfFADCyclohexanone monooxygenase/0.447
4bfuZVUPantothenate kinase2.7.1.330.447
4dliIRGMitogen-activated protein kinase 14/0.447
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.447
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.447
5a4vQUEGlutathione S-transferase F22.5.1.180.447
1h63FMNPentaerythritol tetranitrate reductase/0.446
1uzwCDHIsopenicillin N synthase1.21.3.10.446
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.446
2c27ACOMycothiol acetyltransferase2.3.1.1890.446
2ekaSAHDiphthine synthase/0.446
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.446
2hdjNDPAldo-keto reductase family 1 member C2/0.446
2jb4A14Isopenicillin N synthase1.21.3.10.446
2pksG44Prothrombin3.4.21.50.446
3d7zGK5Mitogen-activated protein kinase 14/0.446
3fwjCAMCamphor 5-monooxygenase1.14.15.10.446
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.446
3vjhJ35Peroxisome proliferator-activated receptor gamma/0.446
4g95OAGDihydrofolate reductase1.5.1.30.446
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.446
4wfr2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
1hb1OCVIsopenicillin N synthase1.21.3.10.445
1itzTPPTransketolase, chloroplastic2.2.1.10.445
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.445
2hk9NAPShikimate dehydrogenase (NADP(+))/0.445
2webPP4Penicillopepsin-13.4.23.200.445
2xdrNDPNAD/NADP-dependent betaine aldehyde dehydrogenase/0.445
3e8xNAPBH1520 protein/0.445
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3l7gM44Xaa-Pro dipeptidase3.4.13.90.445
3lpiZ74Beta-secretase 13.4.23.460.445
3vt7VDXVitamin D3 receptor/0.445
1axwMTXThymidylate synthase/0.444
2c29NAPDihydroflavonol 4-reductase/0.444
2xvv9DNSerum albumin/0.444
2zhf49UProthrombin3.4.21.50.444
3och2MXDihydrofolate reductase1.5.1.30.444
3owuEQUSteroid Delta-isomerase5.3.3.10.444
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3r83Z14Cyclin-dependent kinase 22.7.11.220.444
4dgo0JWCasein kinase II subunit alpha2.7.11.10.444
4exsX8ZMetallo-beta-lactamase type 2/0.444
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.444
4n4v2GYTankyrase-12.4.2.300.444
4ure1PSCyclohexanol dehydrogenase/0.444
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.444
4ykgNADAlkyl hydroperoxide reductase subunit F1.8.10.444
1c7oPPGHemolysin/0.443
1drhNAPDihydrofolate reductase1.5.1.30.443
1ef92CPMethylmalonyl-CoA decarboxylase4.1.1.410.443
1mv8GDXGDP-mannose 6-dehydrogenase1.1.1.1320.443
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.443
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.443
1uh5TCLEnoyl-ACP reductase/0.443
1wxjIPLTryptophan synthase alpha chain/0.443
2bbqPFGThymidylate synthase/0.443
2c42TPPPyruvate synthase/0.443
2e15SAHDiphthine synthase/0.443
2fb35ADGTP 3',8-cyclase4.1.99.180.443
2hg1N5OEndoplasmin/0.443
2rbeZMGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
2rkvZBATrichothecene 3-O-acetyltransferase/0.443
2xlrFADPutative flavin-containing monooxygenase/0.443
3fuj00GLeukotriene A-4 hydrolase3.3.2.60.443
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3ns2PYVAbscisic acid receptor PYL2/0.443
3s41S41Glucokinase2.7.1.20.443
4dhyS41Glucokinase2.7.1.20.443
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.443
4l1xNAPAldo-keto reductase family 1 member C2/0.443
4n3r2GUTankyrase-12.4.2.300.443
4udrFAD5-(hydroxymethyl)furfural oxidase/0.443
1cqp803Integrin alpha-L/0.442
1g8oU5PN-acetyllactosaminide alpha-1,3-galactosyltransferase/0.442
1h51FMNPentaerythritol tetranitrate reductase/0.442
1sreHABStreptavidin/0.442
1srfMTBStreptavidin/0.442
1xlsREARetinoic acid receptor RXR-alpha/0.442
2fr3REACellular retinoic acid-binding protein 2/0.442
2o12FMNChorismate synthase/0.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
3fr5I4AFatty acid-binding protein, adipocyte/0.442
3k99PFTHeat shock protein HSP 90-alpha/0.442
3p62FMNPentaerythritol tetranitrate reductase/0.442
4aoxFADSteroid monooxygenase/0.442
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.442
4bj8BTNAvidin/0.442
4g67SAHUncharacterized ACR, COG1565 superfamily/0.442
4n3l2FNProthrombin3.4.21.50.442
4psbGA3Cytokinin-specific binding protein/0.442
1c0lFADD-amino-acid oxidase1.4.3.30.441
1f8fNADBenzyl alcohol dehydrogenase/0.441
1ie8KH1Vitamin D3 receptor/0.441
1m2rMNYCasein kinase II subunit alpha2.7.11.10.441
1pjcNADAlanine dehydrogenase/0.441
1rq1FADEndoplasmic oxidoreductin-11.8.40.441
1vf2GTXGlutathione S-transferase 32.5.1.180.441
2c3p1TPPyruvate synthase/0.441
2fypRDEEndoplasmin/0.441
2nm2NEUDihydroneopterin aldolase/0.441
2y3sTIRTamL/0.441
3f0aACOSpermidine N(1)-acetyltransferase/0.441
3h2sNDPPutative NADH-flavin reductase/0.441
3lsmSFDPyranose 2-oxidase/0.441
3qt62P0Mevalonate diphosphate decarboxylase/0.441
3rdqDTBStreptavidin/0.441
3v0p4GWHisto-blood group ABO system transferase/0.441
3w8eNAD3-hydroxybutyrate dehydrogenase/0.441
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.441
4fv7E94Mitogen-activated protein kinase 12.7.11.240.441
4yntFDAGlucose oxidase, putative/0.441
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
1diuBDMDihydrofolate reductase1.5.1.30.440
1jtuLYBThymidylate synthase/0.440
1kqgMGDFormate dehydrogenase, nitrate-inducible, major subunit1.1.5.60.440
1tojHCIAspartate aminotransferase2.6.1.10.440
1zdwFLVPrenyltransferase/0.440
2e83FMNFMN-binding protein/0.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.440
2v00V15Endothiapepsin3.4.23.220.440
3dd125DGlycogen phosphorylase, liver form2.4.1.10.440
3ixp834Ecdysone receptor/0.440
3k5gBJCBeta-secretase 13.4.23.460.440
3stuDK3Methylketone synthase I/0.440
4eqsCOACoenzyme A disulfide reductase/0.440
4g2fC07Ephrin type-A receptor 32.7.10.10.440
4jqh1MFAlr2278 protein/0.440
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.440
4q73FADBifunctional protein PutA/0.440
4tvbNADHomospermidine synthase2.5.1.440.440
4wevSUZAldo-keto reductase family 1 member B101.1.10.440
5jadFB2Platelet-activating factor acetylhydrolase3.1.1.470.440