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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
1txtCAAHMG-CoA synthase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1txtCAAHMG-CoA synthase/1.000
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.602
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.593
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.588
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.564
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.559
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.552
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.533
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.487
3l0lHC3Nuclear receptor ROR-gamma/0.485
4a83DXCMajor pollen allergen Bet v 1-A/0.483
1yslCOAHydroxymethylglutaryl-CoA synthase2.3.3.100.482
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.482
2gv8NDPThiol-specific monooxygenase1.14.130.481
3zuyTCHTransporter/0.481
1rekB8LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.480
2hdjNDPAldo-keto reductase family 1 member C2/0.480
1t7o152Carnitine O-acetyltransferase2.3.1.70.478
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.478
4fqsLYAThymidylate synthase ThyA/0.478
4yaiNAIC alpha-dehydrogenase/0.477
4a81DXCMajor pollen allergen Bet v 1-A/0.476
4nxxGDPMitochondrial dynamics protein MID51/0.476
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.476
2vbpVB1Isopenicillin N synthase1.21.3.10.475
1qoqIGPTryptophan synthase alpha chain/0.474
3och2MXDihydrofolate reductase1.5.1.30.472
3h3r14HCollagen type IV alpha-3-binding protein/0.471
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.471
4bb3KKAIsopenicillin N synthase1.21.3.10.470
4v010LIFibroblast growth factor receptor 1 (Fms-related tyrosine kinase 2, Pfeiffer syndrome), isoform CRA_b/0.470
4bfzZVZPantothenate kinase2.7.1.330.469
3t4eNADQuinate/shikimate dehydrogenase/0.468
1obnASVIsopenicillin N synthase1.21.3.10.467
2d29FADAcyl-CoA dehydrogenase/0.467
2jb4A14Isopenicillin N synthase1.21.3.10.467
1gky5GPGuanylate kinase2.7.4.80.466
2iviACWIsopenicillin N synthase1.21.3.10.466
3zeiAWHO-acetylserine sulfhydrylase/0.466
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.466
1uymPU3Heat shock protein HSP 90-beta/0.465
2yee2ECHeat shock protein HSP 90-alpha/0.465
4j7uNAPSepiapterin reductase1.1.1.1530.465
1nvtNAPShikimate dehydrogenase (NADP(+))/0.464
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.464
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.464
3qwbNDPProbable quinone oxidoreductase1.6.5.50.464
1rfuADPPyridoxal kinase2.7.1.350.463
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.463
4knzCB3Thymidylate synthase/0.463
4xo7NAPAldo-keto reductase family 1 member C2/0.463
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.462
1pr9NAPL-xylulose reductase1.1.1.100.461
1x7gNAPPutative ketoacyl reductase1.3.10.460
1xe65FPPlasmepsin-23.4.23.390.460
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.460
3h3qH13Collagen type IV alpha-3-binding protein/0.460
3nmpPYVAbscisic acid receptor PYL2/0.460
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.459
2vcmM11Isopenicillin N synthase1.21.3.10.459
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.459
4rvnCOAPhenylacetate-coenzyme A ligase/0.459
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1xs7MMIBeta-secretase 13.4.23.460.458
2a94AP0L-lactate dehydrogenase1.1.1.270.458
2c29NAPDihydroflavonol 4-reductase/0.458
2q59240Peroxisome proliferator-activated receptor gamma/0.458
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
4jtqNAPAldo-keto reductase family 1 member C2/0.458
1h60STRPentaerythritol tetranitrate reductase/0.457
1j21ATPArgininosuccinate synthase/0.457
1vbiNADMalate/L-lactate dehydrogenase family protein/0.457
2e0nSAHPrecorrin-2 C20-methyltransferase/0.457
2ejzSAHDiphthine synthase/0.457
3c3dFO12-phospho-L-lactate transferase/0.457
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.457
1lf2R37Plasmepsin-23.4.23.390.456
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.456
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.456
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3ohh3HHBeta-secretase 13.4.23.460.456
4bfxZVXPantothenate kinase2.7.1.330.456
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.456
1bk0ACVIsopenicillin N synthase1.21.3.10.455
1h36R88Squalene--hopene cyclase4.2.1.1290.455
2zbaZBATrichothecene 3-O-acetyltransferase/0.455
3fun798Leukotriene A-4 hydrolase3.3.2.60.455
3junAKDPhenazine biosynthesis protein A/B/0.455
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.455
4oztP1AEcdysone receptor, putative/0.455
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.454
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.454
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.454
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.454
4x5hFOLDihydrofolate reductase1.5.1.30.454
1kkq471Peroxisome proliferator-activated receptor alpha/0.453
2e1zB4PPropionate kinase/0.453
2ftoCB3Thymidylate synthase/0.453
2gjlFMNNitronate monooxygenase1.13.12.160.453
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.453
4a802ANMajor pollen allergen Bet v 1-A/0.453
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
1hb1OCVIsopenicillin N synthase1.21.3.10.452
1nzdUPGDNA beta-glucosyltransferase/0.452
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.452
2ed3SAHDiphthine synthase/0.452
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.452
4a3uFMNNADH:flavin oxidoreductase/NADH oxidase/0.452
4a6rTA8Probable aminotransferase/0.452
4ihl1F514-3-3 protein zeta/delta/0.452
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.452
5il2SAHN6-adenosine-methyltransferase 70 kDa subunit/0.452
1a72PADAlcohol dehydrogenase E chain1.1.1.10.451
1blzACVIsopenicillin N synthase1.21.3.10.451
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.451
1udbUFGUDP-glucose 4-epimerase5.1.3.20.451
2cy0NAPShikimate dehydrogenase (NADP(+))/0.451
3f1kNAPUncharacterized oxidoreductase YciK10.451
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4m4922YL-lactate dehydrogenase A chain1.1.1.270.451
1jolFFODihydrofolate reductase1.5.1.30.450
1pq944BOxysterols receptor LXR-beta/0.450
1zdwFLVPrenyltransferase/0.450
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3ft8MOJHeat shock protein HSP 90-alpha/0.450
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
4nxuADPMitochondrial dynamics protein MID51/0.450
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.449
1nzyBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.449
1qiqACCIsopenicillin N synthase1.21.3.10.449
2vbdV10Isopenicillin N synthase1.21.3.10.449
3gwfNAPCyclohexanone monooxygenase/0.449
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.449
3p62FMNPentaerythritol tetranitrate reductase/0.449
4ku5DCC3-oxoacyl-[ACP] synthase III/0.449
1c7oPPGHemolysin/0.448
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.448
1ra8FOLDihydrofolate reductase1.5.1.30.448
1z2iNADPutative malate dehydrogenase/0.448
2p6kSAHDiphthine synthase/0.448
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.448
3p67FMNPentaerythritol tetranitrate reductase/0.448
4l8u9AZSerum albumin/0.448
4q71FADBifunctional protein PutA/0.448
5dp2NAPCurF/0.448
1di8DTQCyclin-dependent kinase 22.7.11.220.447
1fmjRTLRetinol dehydratase/0.447
1kvkATPMevalonate kinase2.7.1.360.447
1uyePU9Heat shock protein HSP 90-alpha/0.447
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.447
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.447
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3gbuATPUncharacterized sugar kinase PH14592.7.10.447
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.447
3up0D7SaceDAF-12/0.447
3vt5YI2Vitamin D3 receptor/0.447
3zoiM2WIsopenicillin N synthase1.21.3.10.447
4dieC5PCytidylate kinase/0.447
4g7gVFVLanosterol 14-alpha-demethylase/0.447
4l4xNDPAmphI/0.447
5eccNAPDehydrofolate reductase type I/0.447
5ej9TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.447
1bwlFMNNADPH dehydrogenase 11.6.99.10.446
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.446
1fm4DXCMajor pollen allergen Bet v 1-L/0.446
1pqc444Oxysterols receptor LXR-beta/0.446
1rneC60Renin3.4.23.150.446
1t2cNAIL-lactate dehydrogenase1.1.1.270.446
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.446
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.446
2xlrFADPutative flavin-containing monooxygenase/0.446
3adaNADSubunit alpha of sarocosine oxidase/0.446
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.446
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.446
3imgBZ2Pantothenate synthetase6.3.2.10.446
3lpiZ74Beta-secretase 13.4.23.460.446
3veu0GOBeta-secretase 13.4.23.460.446
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.446
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.446
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.445
1nqmBTNStreptavidin/0.445
1upw444Oxysterols receptor LXR-beta/0.445
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
2he5NDPAldo-keto reductase family 1 member C211.1.10.445
2ym2NAPPhenylacetone monooxygenase1.14.13.920.445
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
3q8uADPNucleoside diphosphate kinase/0.445
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.445
4ambDUDPutative glycosyl transferase/0.445
4jq3NAPAldo-keto reductase family 1 member C2/0.445
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.445
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.444
1o9bNAIQuinate/shikimate dehydrogenase/0.444
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.444
1uyhPU0Heat shock protein HSP 90-alpha/0.444
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.444
2e8sSAHDiphthine synthase/0.444
2hveADPNucleoside diphosphate kinase A2.7.4.60.444
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.444
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.444
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
3hl0NADMaleylacetate reductase/0.444
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3toxNAPPutative oxidoreductase/0.444
4a862ANMajor pollen allergen Bet v 1-A/0.444
4dbzNDPPutative ketoacyl reductase1.3.10.444
4e5kNADPhosphonate dehydrogenase1.20.1.10.444
4imfSI3N-acetylneuraminate lyase/0.444
4lxk1YTBeta-secretase 13.4.23.460.444
5irnADPNucleotide binding oligomerization domain containing 2/0.444
1aiqCB3Thymidylate synthase/0.443
1udaUFGUDP-glucose 4-epimerase5.1.3.20.443
2c27ACOMycothiol acetyltransferase2.3.1.1890.443
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.443
3d91REMRenin3.4.23.150.443
3ful52DLeukotriene A-4 hydrolase3.3.2.60.443
3if9FADGlycine oxidase1.4.3.190.443
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.443
3tqxPLP2-amino-3-ketobutyrate coenzyme A ligase/0.443
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.443
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.443
4ipw1G7Mycocyclosin synthase1.14.21.90.443
4jicFMNGTN Reductase/0.443
1drbMTXDihydrofolate reductase1.5.1.30.442
1icpFMN12-oxophytodienoate reductase 11.3.1.420.442
1ppjANYCytochrome b/0.442
1vi2NADQuinate/shikimate dehydrogenase/0.442
1xddAAYIntegrin alpha-L/0.442
1xe55FEPlasmepsin-23.4.23.390.442
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.442
2dshSAHDiphthine synthase/0.442
2eeqSAHDiphthine synthase/0.442
2hfuMEVMevalonate kinase/0.442
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
2whqHI6Acetylcholinesterase3.1.1.70.442
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4bfvZVVPantothenate kinase2.7.1.330.442
4h9tHL4Phosphotriesterase/0.442
4j7xNAPSepiapterin reductase1.1.1.1530.442
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.442
4kugNAD3-hydroxybutyryl-CoA dehydrogenase/0.442
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.442
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
4xr9NADCalS8/0.442
1d3dBZTProthrombin3.4.21.50.441
1dyjDDFDihydrofolate reductase1.5.1.30.441
1ex75GPGuanylate kinase2.7.4.80.441
1f8fNADBenzyl alcohol dehydrogenase/0.441
1w4zNAPPutative ketoacyl reductase1.3.10.441
1w6jR71Lanosterol synthase5.4.99.70.441
1x27ASP_ASP_TYR_VAL_PTRTyrosine-protein kinase Lck2.7.10.20.441
1x2hLPALipoate-protein ligase A6.3.1.200.441
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.441
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.441
2ociTYCValacyclovir hydrolase3.10.441
2po7CHDFerrochelatase, mitochondrial4.99.1.10.441
2rg5279Mitogen-activated protein kinase 14/0.441
3c35KAIGlutamate receptor ionotropic, kainate 1/0.441
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.441
3f03FMNPentaerythritol tetranitrate reductase/0.441
3gwdNAPCyclohexanone monooxygenase/0.441
4a86H35Major pollen allergen Bet v 1-A/0.441
4dbc3QPAspartate aminotransferase2.6.1.10.441
4dvi2IWTankyrase-12.4.2.300.441
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.441
4hwkNAPSepiapterin reductase1.1.1.1530.441
4jlj1NMDeoxycytidine kinase2.7.1.740.441
4mlp2CXCryptochrome-2/0.441
5uviZMAAdenosine receptor A2a/0.441
1dnaCB3Thymidylate synthase/0.440
1e1kFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.440
1e3lNADAlcohol dehydrogenase 41.1.1.10.440
1hfqMOTDihydrofolate reductase1.5.1.30.440
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.440
2y3rTRKTamL/0.440
2y60M8FIsopenicillin N synthase1.21.3.10.440
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.440
3atzFMNProstaglandin F2a synthase/0.440
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3gwfFADCyclohexanone monooxygenase/0.440
3qlrNDPDihydrofolate reductase1.5.1.30.440
3r96ACOMccE protein/0.440
3s1dZIRCytokinin dehydrogenase 11.5.99.120.440
3wqmB29Diterpene synthase3.1.7.80.440
4g3jVNTLanosterol 14-alpha-demethylase/0.440
4hyvPEPPyruvate kinase 12.7.1.400.440