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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
1txtCAAHMG-CoA synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
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
2hdjNDPAldo-keto reductase family 1 member C2/0.491
2vkeTACTetracycline repressor protein class D/0.490
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.489
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.487
2jb4A14Isopenicillin N synthase1.21.3.10.487
3zuyTCHTransporter/0.487
2gv8NDPThiol-specific monooxygenase1.14.130.486
2d29FADAcyl-CoA dehydrogenase/0.484
1yslCOAHydroxymethylglutaryl-CoA synthase2.3.3.100.482
4yaiNAIC alpha-dehydrogenase/0.482
3zeiAWHO-acetylserine sulfhydrylase/0.480
2iviACWIsopenicillin N synthase1.21.3.10.479
2vbpVB1Isopenicillin N synthase1.21.3.10.479
3g72A6TRenin3.4.23.150.479
4bb3KKAIsopenicillin N synthase1.21.3.10.479
4fqsLYAThymidylate synthase ThyA/0.478
1obnASVIsopenicillin N synthase1.21.3.10.477
4ambDUDPutative glycosyl transferase/0.477
4nxxGDPMitochondrial dynamics protein MID51/0.477
3h3r14HCollagen type IV alpha-3-binding protein/0.475
4bfzZVZPantothenate kinase2.7.1.330.475
3qwbNDPProbable quinone oxidoreductase1.6.5.50.474
4ipw1G7Mycocyclosin synthase1.14.21.90.474
1hb3SCVIsopenicillin N synthase1.21.3.10.473
3b9oFMNAlkane monoxygenase/0.473
1uymPU3Heat shock protein HSP 90-beta/0.472
4j7uNAPSepiapterin reductase1.1.1.1530.472
4xo7NAPAldo-keto reductase family 1 member C2/0.472
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
4g7gVFVLanosterol 14-alpha-demethylase/0.468
1qiqACCIsopenicillin N synthase1.21.3.10.467
3l0lHC3Nuclear receptor ROR-gamma/0.467
4knzCB3Thymidylate synthase/0.467
1bk0ACVIsopenicillin N synthase1.21.3.10.466
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.466
1rfuADPPyridoxal kinase2.7.1.350.466
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.465
3h3qH13Collagen type IV alpha-3-binding protein/0.465
4g3jVNTLanosterol 14-alpha-demethylase/0.465
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.465
4mlp2CXCryptochrome-2/0.465
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.464
4nieNBHNuclear receptor ROR-gamma/0.464
4nxuADPMitochondrial dynamics protein MID51/0.464
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.463
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.463
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.463
3uylTYDProbable NDP-rhamnosyltransferase/0.462
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.462
1c7oPPGHemolysin/0.461
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1e3lNADAlcohol dehydrogenase 41.1.1.10.461
2vbdV10Isopenicillin N synthase1.21.3.10.461
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.461
3k1wBFXRenin3.4.23.150.461
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
1blzACVIsopenicillin N synthase1.21.3.10.460
2x7hPFNProstaglandin reductase 310.460
3b70NAPEnoyl reductase LovC10.460
3zkyWT4Isopenicillin N synthase1.21.3.10.460
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
1e3eNAIAlcohol dehydrogenase 41.1.1.10.459
1pqc444Oxysterols receptor LXR-beta/0.459
1xs7MMIBeta-secretase 13.4.23.460.459
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.459
2vcmM11Isopenicillin N synthase1.21.3.10.459
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.459
4zowCLMMultidrug transporter MdfA/0.459
1hb1OCVIsopenicillin N synthase1.21.3.10.458
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.458
1ppjANYCytochrome b/0.458
2c29NAPDihydroflavonol 4-reductase/0.458
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3ohh3HHBeta-secretase 13.4.23.460.458
5irnADPNucleotide binding oligomerization domain containing 2/0.458
1lf2R37Plasmepsin-23.4.23.390.457
1zdwFLVPrenyltransferase/0.457
4ihl1F514-3-3 protein zeta/delta/0.457
4l9kEHFSerum albumin/0.457
1h36R88Squalene--hopene cyclase4.2.1.1290.456
1pr9NAPL-xylulose reductase1.1.1.100.456
1vbiNADMalate/L-lactate dehydrogenase family protein/0.456
1zg32HIIsoflavone 4'-O-methyltransferase/0.456
2e0nSAHPrecorrin-2 C20-methyltransferase/0.456
2g247IGRenin3.4.23.150.456
3zoiM2WIsopenicillin N synthase1.21.3.10.456
4jq3NAPAldo-keto reductase family 1 member C2/0.456
4ku5DCC3-oxoacyl-[ACP] synthase III/0.456
1xe55FEPlasmepsin-23.4.23.390.455
2ftoCB3Thymidylate synthase/0.455
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.455
2zbaZBATrichothecene 3-O-acetyltransferase/0.455
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4oztP1AEcdysone receptor, putative/0.455
1kkq471Peroxisome proliferator-activated receptor alpha/0.454
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.454
1upw444Oxysterols receptor LXR-beta/0.454
2e1zB4PPropionate kinase/0.454
3tdaPN0Cytochrome P450 2D6/0.454
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1dliUDXUDP-glucose 6-dehydrogenase/0.453
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.453
1uyePU9Heat shock protein HSP 90-alpha/0.453
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.453
2po7CHDFerrochelatase, mitochondrial4.99.1.10.453
3f3sNADLambda-crystallin homolog/0.453
3toxNAPPutative oxidoreductase/0.453
4a83DXCMajor pollen allergen Bet v 1-A/0.453
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.453
5ej4TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.453
1nzdUPGDNA beta-glucosyltransferase/0.452
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.452
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.452
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
4bfxZVXPantothenate kinase2.7.1.330.452
1cscCMCCitrate synthase, mitochondrial2.3.3.10.451
1j21ATPArgininosuccinate synthase/0.451
1ojtFADDihydrolipoyl dehydrogenase/0.451
1w4zNAPPutative ketoacyl reductase1.3.10.451
2e9cB75Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.451
2pobGW4Peroxisome proliferator-activated receptor gamma/0.451
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.451
4a81DXCMajor pollen allergen Bet v 1-A/0.451
4dieC5PCytidylate kinase/0.451
4jlj1NMDeoxycytidine kinase2.7.1.740.451
4l1xNAPAldo-keto reductase family 1 member C2/0.451
5dp2NAPCurF/0.451
1f8fNADBenzyl alcohol dehydrogenase/0.450
1rneC60Renin3.4.23.150.450
2oz57XYUncharacterized protein/0.450
2xlrFADPutative flavin-containing monooxygenase/0.450
3adaNADSubunit alpha of sarocosine oxidase/0.450
3ft8MOJHeat shock protein HSP 90-alpha/0.450
4e5kNADPhosphonate dehydrogenase1.20.1.10.450
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.450
4m9aFDAAcyl-CoA dehydrogenase/0.450
4r20AERCytochrome P450 family 17 polypeptide 2/0.450
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
1icpFMN12-oxophytodienoate reductase 11.3.1.420.449
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.449
2y60M8FIsopenicillin N synthase1.21.3.10.449
2ym2NAPPhenylacetone monooxygenase1.14.13.920.449
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3gbuATPUncharacterized sugar kinase PH14592.7.10.449
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
4cdmFO1Deoxyribodipyrimidine photolyase/0.449
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.449
4j7xNAPSepiapterin reductase1.1.1.1530.449
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.449
4o1mNADEnoyl-acyl carrier reductase/0.449
4ryvZEAProtein LlR18A/0.449
1di8DTQCyclin-dependent kinase 22.7.11.220.448
1pq944BOxysterols receptor LXR-beta/0.448
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3g70A5TRenin3.4.23.150.448
3p67FMNPentaerythritol tetranitrate reductase/0.448
3r96ACOMccE protein/0.448
4frkDWDBeta-secretase 13.4.23.460.448
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.448
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.448
4hwkNAPSepiapterin reductase1.1.1.1530.448
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.448
4q71FADBifunctional protein PutA/0.448
5uviZMAAdenosine receptor A2a/0.448
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.447
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.447
1kvkATPMevalonate kinase2.7.1.360.447
1xddAAYIntegrin alpha-L/0.447
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.447
2gjlFMNNitronate monooxygenase1.13.12.160.447
2hveADPNucleoside diphosphate kinase A2.7.4.60.447
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.447
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.447
3junAKDPhenazine biosynthesis protein A/B/0.447
3lpiZ74Beta-secretase 13.4.23.460.447
3oadLPORenin3.4.23.150.447
3up0D7SaceDAF-12/0.447
3vt5YI2Vitamin D3 receptor/0.447
3wbwNDPPutative 2,5-diketo-D-gluconic acid reductase/0.447
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
4dc0NDPPutative ketoacyl reductase1.3.10.447
4qe6JN3Bile acid receptor/0.447
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.446
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.446
2he5NDPAldo-keto reductase family 1 member C211.1.10.446
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3nmpPYVAbscisic acid receptor PYL2/0.446
3q8uADPNucleoside diphosphate kinase/0.446
3veu0GOBeta-secretase 13.4.23.460.446
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.446
4e5nNADPhosphonate dehydrogenase1.20.1.10.446
4irnFADAnaB/0.446
4nbwNADShort-chain dehydrogenase/reductase SDR/0.446
1j49NADD-lactate dehydrogenase1.1.1.280.445
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.445
1rsgFADPolyamine oxidase FMS1/0.445
1u1cBAUUridine phosphorylase2.4.2.30.445
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.445
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.445
2g1s4IGRenin3.4.23.150.445
2y6fM9FIsopenicillin N synthase1.21.3.10.445
3f63GTXGlutathione transferase GST1-4/0.445
3jpuTY4Transcriptional activator protein LasR/0.445
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.445
3zhtTD9Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.445
4a6rTA8Probable aminotransferase/0.445
4a862ANMajor pollen allergen Bet v 1-A/0.445
4bfvZVVPantothenate kinase2.7.1.330.445
4dpf0LGBeta-secretase 13.4.23.460.445
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
4lxk1YTBeta-secretase 13.4.23.460.445
1aiqCB3Thymidylate synthase/0.444
1jipKTN6-deoxyerythronolide B hydroxylase/0.444
2ikuLIYRenin3.4.23.150.444
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
3imgBZ2Pantothenate synthetase6.3.2.10.444
4a802ANMajor pollen allergen Bet v 1-A/0.444
4b2gV1NUncharacterized protein/0.444
4dbzNDPPutative ketoacyl reductase1.3.10.444
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.444
4kwhNAPReductase homolog/0.444
1khrVIRStreptogramin A acetyltransferase2.3.10.443
1w6hTITPlasmepsin-23.4.23.390.443
2bu9HFVIsopenicillin N synthase1.21.3.10.443
2c27ACOMycothiol acetyltransferase2.3.1.1890.443
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.443
2dteNAIGlucose 1-dehydrogenase related protein/0.443
2dxdANPNucleoside diphosphate kinase2.7.4.60.443
2e9dB76Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.443
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.443
2il2LIXRenin3.4.23.150.443
2nq8ZIDEnoyl-ACP reductase/0.443
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.443
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3gwdNAPCyclohexanone monooxygenase/0.443
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.443
3if9FADGlycine oxidase1.4.3.190.443
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.443
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
4ez8DHFThymidylate synthase2.1.1.450.443
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4kbyC2EStimulator of interferon genes protein/0.443
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4yagNAIC alpha-dehydrogenase/0.443
1d3dBZTProthrombin3.4.21.50.442
1fm4DXCMajor pollen allergen Bet v 1-L/0.442
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.442
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.442
1x7hNDPPutative ketoacyl reductase1.3.10.442
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.442
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2g1n1IGRenin3.4.23.150.442
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
3h3sH15Collagen type IV alpha-3-binding protein/0.442
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3lqfNADGalactitol dehydrogenase/0.442
3p74FMNPentaerythritol tetranitrate reductase/0.442
3rucNADUDP-N-acetylglucosamine 4-epimerase/0.442
4eb7PLPCysteine desulfurase IscS 2/0.442
4h3j10WBeta-secretase 13.4.23.460.442
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.442
4req5ADMethylmalonyl-CoA mutase large subunit5.4.99.20.442
1hfqMOTDihydrofolate reductase1.5.1.30.441
1qjfACSIsopenicillin N synthase1.21.3.10.441
1w6jR71Lanosterol synthase5.4.99.70.441
2g1y5IGRenin3.4.23.150.441
2hq9FADMll6688 protein/0.441
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.441
2rg5279Mitogen-activated protein kinase 14/0.441
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
2xgs44PUncharacterized protein/0.441
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.441
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.441
4dvi2IWTankyrase-12.4.2.300.441
4i6gFADCryptochrome-2/0.441
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
1adfTADAlcohol dehydrogenase E chain1.1.1.10.440
1d3pBT3Prothrombin3.4.21.50.440
1dnaCB3Thymidylate synthase/0.440
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.440
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
1p0ySAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.440
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.440
1uy9PU6Heat shock protein HSP 90-alpha/0.440
1xe65FPPlasmepsin-23.4.23.390.440
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.440
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.440
2fznFADBifunctional protein PutA1.5.5.20.440
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.440
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.440
2o12FMNChorismate synthase/0.440
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.440
3drcMTXDihydrofolate reductase1.5.1.30.440
3q43D66M1 family aminopeptidase3.4.110.440
3vthAPCCarbamoyltransferase/0.440
4da7AC2Purine nucleoside phosphorylase DeoD-type2.4.2.10.440
4fco0U4Beta-secretase 13.4.23.460.440
4iarERM5-hydroxytryptamine receptor 1B/0.440
4jx1CAHCamphor 5-monooxygenase1.14.15.10.440
4l5b1UXDeoxycytidine kinase2.7.1.740.440
5d3qGDPDynamin-13.6.5.50.440
5jlaNADPutative short-chain dehydrogenase/reductase/0.440
5kwvANPPantothenate synthetase/0.440