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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
5hwrCOAHydroxymethylglutaryl-CoA synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
5hwrCOAHydroxymethylglutaryl-CoA synthase/1.000
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.768
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.681
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.616
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.589
1txtCAAHMG-CoA synthase/0.574
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.542
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.514
4twnB96Ephrin type-A receptor 32.7.10.10.499
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.495
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.488
1vbiNADMalate/L-lactate dehydrogenase family protein/0.487
2g8yNADHydroxycarboxylate dehydrogenase B/0.482
2gv8NDPThiol-specific monooxygenase1.14.130.482
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.475
3p62FMNPentaerythritol tetranitrate reductase/0.475
1rfvADPPyridoxal kinase2.7.1.350.474
1yslCOAHydroxymethylglutaryl-CoA synthase2.3.3.100.474
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.474
4bfxZVXPantothenate kinase2.7.1.330.474
3uylTYDProbable NDP-rhamnosyltransferase/0.473
2y0mACOHistone acetyltransferase KAT8/0.472
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.472
4ambDUDPutative glycosyl transferase/0.472
5dmhADP3-oxo-tetronate kinase/0.472
2vcmM11Isopenicillin N synthase1.21.3.10.471
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
1upw444Oxysterols receptor LXR-beta/0.468
2iviACWIsopenicillin N synthase1.21.3.10.468
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.468
4q71FADBifunctional protein PutA/0.468
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.467
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.467
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.467
2po7CHDFerrochelatase, mitochondrial4.99.1.10.465
4yaiNAIC alpha-dehydrogenase/0.465
1r5hAO2Methionine aminopeptidase 2/0.464
4uyf73BBromodomain-containing protein 2/0.464
2xvw9NRSerum albumin/0.463
1culFOKAdenylate cyclase type 2/0.462
1culFOKAdenylate cyclase type 5/0.462
1psa0ZLPepsin A3.4.23.10.462
2dv3SAHDiphthine synthase/0.462
1ay0TPPTransketolase 12.2.1.10.461
1drhNAPDihydrofolate reductase1.5.1.30.461
2gjlFMNNitronate monooxygenase1.13.12.160.461
2ym2NAPPhenylacetone monooxygenase1.14.13.920.461
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3pqbVGPPutative oxidoreductase/0.461
3b9oFMNAlkane monoxygenase/0.460
1adfTADAlcohol dehydrogenase E chain1.1.1.10.459
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
2wo7ASVIsopenicillin N synthase1.21.3.10.459
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.459
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.459
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
2e15SAHDiphthine synthase/0.458
2vbdV10Isopenicillin N synthase1.21.3.10.458
2vbpVB1Isopenicillin N synthase1.21.3.10.458
4ead0NPThymidine phosphorylase2.4.2.40.458
4mlp2CXCryptochrome-2/0.458
5dp2NAPCurF/0.458
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.457
3nbvANPKetohexokinase/0.457
3tneRITCandidapepsin-13.4.23.240.457
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.457
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.457
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.456
2z6rSAHDiphthine synthase/0.456
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3vdqNAD3-hydroxybutyrate dehydrogenase/0.456
4jx1CAHCamphor 5-monooxygenase1.14.15.10.456
4nxxGDPMitochondrial dynamics protein MID51/0.456
4u9aSTUInterleukin-1 receptor-associated kinase 42.7.11.10.456
1qiqACCIsopenicillin N synthase1.21.3.10.455
2bu9HFVIsopenicillin N synthase1.21.3.10.455
2hdjNDPAldo-keto reductase family 1 member C2/0.455
3h3qH13Collagen type IV alpha-3-binding protein/0.455
3lqfNADGalactitol dehydrogenase/0.455
1lf2R37Plasmepsin-23.4.23.390.454
1uzwCDHIsopenicillin N synthase1.21.3.10.454
1xddAAYIntegrin alpha-L/0.454
3d7zGK5Mitogen-activated protein kinase 14/0.454
3ft8MOJHeat shock protein HSP 90-alpha/0.454
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.454
3lpkZ76Beta-secretase 13.4.23.460.454
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.454
1kr2TADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.453
1me6IVSPlasmepsin-23.4.23.390.453
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
3b6zCO7Enoyl reductase LovC10.453
3cib314Beta-secretase 13.4.23.460.453
3k5gBJCBeta-secretase 13.4.23.460.453
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.453
1blzACVIsopenicillin N synthase1.21.3.10.452
1uymPU3Heat shock protein HSP 90-beta/0.452
2pg0FADAcyl-CoA dehydrogenase/0.452
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.452
2rqfJH3Hemolymph juvenile hormone binding protein/0.452
2x7hPFNProstaglandin reductase 310.452
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3t3r9PLCytochrome P450 2A61.14.130.452
4a83DXCMajor pollen allergen Bet v 1-A/0.452
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.451
2wezZYEBeta-secretase 13.4.23.460.451
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.451
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
4bftZVTPantothenate kinase2.7.1.330.451
4dbzNDPPutative ketoacyl reductase1.3.10.451
5irnADPNucleotide binding oligomerization domain containing 2/0.451
1h50FMNPentaerythritol tetranitrate reductase/0.450
1kvkATPMevalonate kinase2.7.1.360.450
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.450
1u4oNDDL-lactate dehydrogenase1.1.1.270.450
2c29NAPDihydroflavonol 4-reductase/0.450
2xvv9DNSerum albumin/0.450
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3lpiZ74Beta-secretase 13.4.23.460.450
3zxzKRWHepatocyte growth factor receptor2.7.10.10.450
4hy6FJ1Heat shock protein HSP 90-alpha/0.450
4l9kEHFSerum albumin/0.450
4r81FMNPredicted NADH dehydrogenase/0.450
5c77SAHProtein arginine N-methyltransferase SFM1/0.450
5ej9TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.450
5jlaNADPutative short-chain dehydrogenase/reductase/0.450
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1r2jFADFkbI/0.449
1uyePU9Heat shock protein HSP 90-alpha/0.449
3qe2FMNNADPH--cytochrome P450 reductase/0.449
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.449
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
5fl3ADPPili retraction protein PilT/0.449
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.448
1hb1OCVIsopenicillin N synthase1.21.3.10.448
1obnASVIsopenicillin N synthase1.21.3.10.448
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.448
2p6lSAHDiphthine synthase/0.448
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
3da24MDCarbonic anhydrase 134.2.1.10.448
3ibdCPZCytochrome P450 2B61.14.130.448
3ohh3HHBeta-secretase 13.4.23.460.448
3zkyWT4Isopenicillin N synthase1.21.3.10.448
4bb3KKAIsopenicillin N synthase1.21.3.10.448
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.448
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.448
4bfsZVSPantothenate kinase2.7.1.330.448
4ipw1G7Mycocyclosin synthase1.14.21.90.448
4oztP1AEcdysone receptor, putative/0.448
4q73FADBifunctional protein PutA/0.448
1h51FMNPentaerythritol tetranitrate reductase/0.447
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.447
1kqwRTLCellular retinol-binding protein type II/0.447
1rfuADPPyridoxal kinase2.7.1.350.447
2e0nSAHPrecorrin-2 C20-methyltransferase/0.447
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.447
2g78REACellular retinoic acid-binding protein 2/0.447
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1qzyTDEMethionine aminopeptidase 2/0.446
1r5gAO1Methionine aminopeptidase 2/0.446
2eeqSAHDiphthine synthase/0.446
2ejzSAHDiphthine synthase/0.446
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.446
2jb4A14Isopenicillin N synthase1.21.3.10.446
2y6fM9FIsopenicillin N synthase1.21.3.10.446
3f03FMNPentaerythritol tetranitrate reductase/0.446
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.446
3toxNAPPutative oxidoreductase/0.446
3vf60H6Glucokinase2.7.1.20.446
4ap1NAPSteroid monooxygenase/0.446
4dc1NDPPutative ketoacyl reductase1.3.10.446
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.446
1fmlRTLRetinol dehydratase/0.445
1geeNADGlucose 1-dehydrogenase1.1.1.470.445
1iy8NADLevodione reductase/0.445
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1kceCB3Thymidylate synthase/0.445
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.445
1u3dFADCryptochrome-1/0.445
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.445
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2il2LIXRenin3.4.23.150.445
2owuSAHDiphthine synthase/0.445
2rlcCHDCholoylglycine hydrolase3.5.1.240.445
3duyAFJBeta-secretase 13.4.23.460.445
3oquA8SAbscisic acid receptor PYL9/0.445
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.445
1a72PADAlcohol dehydrogenase E chain1.1.1.10.444
1bim0QBRenin3.4.23.150.444
1f5fDHTSex hormone-binding globulin/0.444
1qjfACSIsopenicillin N synthase1.21.3.10.444
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.444
1tysTMPThymidylate synthase/0.444
1x7hNDPPutative ketoacyl reductase1.3.10.444
2h55DZ8Heat shock protein HSP 90-alpha/0.444
2huvSAHDiphthine synthase/0.444
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.444
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.444
2oz57XYUncharacterized protein/0.444
2wdzNADGalactitol dehydrogenase/0.444
2ztlNADD(-)-3-hydroxybutyrate dehydrogenase/0.444
3b9lAZZSerum albumin/0.444
3hl0NADMaleylacetate reductase/0.444
4an4DUDPutative glycosyl transferase/0.444
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.444
4i5eNAPAlclohol dehydrogenase/short-chain dehydrogenase/0.444
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.444
4n3r2GUTankyrase-12.4.2.300.444
4nxuADPMitochondrial dynamics protein MID51/0.444
4tuvCPZCytochrome P450 1191.140.444
5dldUD1UDP-N-Acetylglucosamine 2-epimerase/0.444
1fm4DXCMajor pollen allergen Bet v 1-L/0.443
1hb3SCVIsopenicillin N synthase1.21.3.10.443
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.443
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.443
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.443
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.443
2z6cFMNPhototropin-12.7.11.10.443
3gw9VNILanosterol 14-alpha-demethylase/0.443
3o6o94MHeat shock protein 83/0.443
3oetNADErythronate-4-phosphate dehydrogenase/0.443
4ku5DCC3-oxoacyl-[ACP] synthase III/0.443
5a3bAPRSIR2 family protein/0.443
1bk0ACVIsopenicillin N synthase1.21.3.10.442
1ia1NDPDihydrofolate reductase1.5.1.30.442
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
1pq944BOxysterols receptor LXR-beta/0.442
1rwbNADGlucose 1-dehydrogenase1.1.1.470.442
1tehNADAlcohol dehydrogenase class-31.1.1.10.442
2dv7SAHDiphthine synthase/0.442
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.442
2ydvNECAdenosine receptor A2a/0.442
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.442
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.442
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.442
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
5jqhCAUBeta-2 adrenergic receptor/0.442
1gcoNADGlucose 1-dehydrogenase1.1.1.470.441
2a4xBLMMitomycin-binding protein/0.441
2eglSAHDiphthine synthase/0.441
2givACOHistone acetyltransferase KAT8/0.441
2gqpPA7Endoplasmin/0.441
2p6kSAHDiphthine synthase/0.441
3adaNADSubunit alpha of sarocosine oxidase/0.441
3clsFADElectron transfer flavoprotein subunit alpha/0.441
3h3sH15Collagen type IV alpha-3-binding protein/0.441
3oibFDAPutative acyl-CoA dehydrogenase/0.441
3up4NAP2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.441
3w0c6DSVitamin D3 receptor/0.441
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.441
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.441
4iarERM5-hydroxytryptamine receptor 1B/0.441
4qi5FADCellobiose dehydrogenase/0.441
4rheFMNFlavin prenyltransferase UbiX/0.441
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
4yvkSFGtRNA (guanine-N(1)-)-methyltransferase2.1.1.2280.441
1j7kATPHolliday junction ATP-dependent DNA helicase RuvB/0.440
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.440
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.440
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2draATPCCA-adding enzyme2.7.7.720.440
2dv5SAHDiphthine synthase/0.440
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.440
2g247IGRenin3.4.23.150.440
2ikuLIYRenin3.4.23.150.440
2p9dSAHDiphthine synthase/0.440
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.440
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.440
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.440
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3f3sNADLambda-crystallin homolog/0.440
3sf6FDAGlutaryl-CoA dehydrogenase/0.440
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.440
4dvi2IWTankyrase-12.4.2.300.440
4g7gVFVLanosterol 14-alpha-demethylase/0.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.440
4plpNADHomospermidine synthase2.5.1.440.440
4u0mGTPCyclic GMP-AMP synthase/0.440
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.440
5js6NAD17-beta-hydroxysteroid dehydrogenase 141.1.10.440