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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
3qt62P0Mevalonate diphosphate decarboxylase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3qt62P0Mevalonate diphosphate decarboxylase/1.000
4dptAGSMevalonate diphosphate decarboxylase/0.582
4dpy2P0Mevalonate diphosphate decarboxylase/0.580
4dpuAGSMevalonate diphosphate decarboxylase/0.552
4du82P0Mevalonate diphosphate decarboxylase/0.544
1xddAAYIntegrin alpha-L/0.500
1xe55FEPlasmepsin-23.4.23.390.491
3bk2U5PRibonuclease J/0.491
2oapANPType II secretion system protein (GspE-2)/0.489
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.488
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.486
1c7oPPGHemolysin/0.485
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.485
1xe65FPPlasmepsin-23.4.23.390.483
3wqmB29Diterpene synthase3.1.7.80.482
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.480
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.480
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.479
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.478
1udaUFGUDP-glucose 4-epimerase5.1.3.20.477
2g1n1IGRenin3.4.23.150.477
3lqfNADGalactitol dehydrogenase/0.474
1bwsNDPGDP-L-fucose synthase/0.473
1xvaSAMGlycine N-methyltransferase2.1.1.200.473
2g1s4IGRenin3.4.23.150.473
2rlcCHDCholoylglycine hydrolase3.5.1.240.473
3gw9VNILanosterol 14-alpha-demethylase/0.473
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.472
1bil0IURenin3.4.23.150.471
2zbaZBATrichothecene 3-O-acetyltransferase/0.471
4jicFMNGTN Reductase/0.471
1psa0ZLPepsin A3.4.23.10.470
2dftADPShikimate kinase2.7.1.710.469
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.469
4g7gVFVLanosterol 14-alpha-demethylase/0.469
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.468
2gv8NDPThiol-specific monooxygenase1.14.130.468
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.468
3p74FMNPentaerythritol tetranitrate reductase/0.468
3tjzGNPADP-ribosylation factor 1/0.468
4yvz3ATDNA integrity scanning protein DisA/0.468
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.467
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.467
3s1dZIRCytokinin dehydrogenase 11.5.99.120.467
3af1GDPPantothenate kinase2.7.1.330.466
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.466
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.466
4nieNBHNuclear receptor ROR-gamma/0.466
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.465
1n3rGTPGTP cyclohydrolase 13.5.4.160.464
3phiNDPShikimate dehydrogenase (NADP(+))/0.464
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.463
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.463
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.463
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.463
3p62FMNPentaerythritol tetranitrate reductase/0.463
4g3jVNTLanosterol 14-alpha-demethylase/0.463
4xguADPPutative pachytene checkpoint protein 2/0.463
4i1iNADMalate dehydrogenase/0.462
3tr05GPGuanylate kinase/0.461
4nbwNADShort-chain dehydrogenase/reductase SDR/0.461
5a3bAPRSIR2 family protein/0.461
1f8fNADBenzyl alcohol dehydrogenase/0.460
2g1o2IGRenin3.4.23.150.460
2uxoTACHTH-type transcriptional regulator TtgR/0.460
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.460
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.460
3rsv3RSBeta-secretase 13.4.23.460.460
4a83DXCMajor pollen allergen Bet v 1-A/0.460
4wecNADShort chain dehydrogenase/0.460
1vf3GDNGlutathione S-transferase 32.5.1.180.459
2ejvNADL-threonine 3-dehydrogenase/0.459
2iyfERYOleandomycin glycosyltransferase2.4.10.459
3own3OWRenin3.4.23.150.459
4bfzZVZPantothenate kinase2.7.1.330.459
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.459
1lbcCYZGlutamate receptor 2/0.458
1obbNADAlpha-glucosidase3.2.1.200.458
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.458
2g247IGRenin3.4.23.150.458
2ikuLIYRenin3.4.23.150.458
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.458
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.458
4ipw1G7Mycocyclosin synthase1.14.21.90.458
2a94AP0L-lactate dehydrogenase1.1.1.270.457
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.457
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.457
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.457
3b70NAPEnoyl reductase LovC10.457
3ieuGDPGTPase Era/0.457
3nxxNDPDihydrofolate reductase1.5.1.30.457
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.457
1u1gBBBUridine phosphorylase2.4.2.30.456
2gjlFMNNitronate monooxygenase1.13.12.160.456
2i4qUA4Renin3.4.23.150.456
3eksCY9Actin-5C/0.456
1qrpHH0Pepsin A-43.4.23.10.455
3af0GDPPantothenate kinase2.7.1.330.455
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.455
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4g090VDHistidinol dehydrogenase/0.455
4gl4NAIAlcohol dehydrogenase class-3/0.455
1fy7COAHistone acetyltransferase ESA1/0.454
1x1aSAMC-20 methyltransferase/0.454
2cftPLPPyridoxal phosphate phosphatase/0.454
2ea2F77Methionine aminopeptidase 2/0.454
2he5NDPAldo-keto reductase family 1 member C211.1.10.454
2ifaFMNUncharacterized protein/0.454
2r0cFADPutative FAD-monooxygenase/0.454
2rcyNAPPyrroline-5-carboxylate reductase/0.454
3atzFMNProstaglandin F2a synthase/0.454
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.454
3p82FMNPentaerythritol tetranitrate reductase/0.454
4q71FADBifunctional protein PutA/0.454
1dr2TAPDihydrofolate reductase1.5.1.30.453
1h51FMNPentaerythritol tetranitrate reductase/0.453
1nl4HFPProtein farnesyltransferase subunit beta2.5.1.580.453
1tehNADAlcohol dehydrogenase class-31.1.1.10.453
2a7r5GPGMP reductase 2/0.453
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.453
2qbuSAHPrecorrin-2 methyltransferase/0.453
3b6zCO7Enoyl reductase LovC10.453
3c212BADNA integrity scanning protein DisA/0.453
3d91REMRenin3.4.23.150.453
4a6nFADTetX family tetracycline inactivation enzyme/0.453
4rvfTYDD-mycarose 3-C-methyltransferase/0.453
4v2gITCTetracycline repressor protein class D/0.453
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.452
2qimZEAClass 10 plant pathogenesis-related protein/0.452
3r7kFDAProbable acyl CoA dehydrogenase/0.452
5ftfADPTPR domain protein/0.452
1h63FMNPentaerythritol tetranitrate reductase/0.451
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.451
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
3f03FMNPentaerythritol tetranitrate reductase/0.451
3h3qH13Collagen type IV alpha-3-binding protein/0.451
3uylTYDProbable NDP-rhamnosyltransferase/0.451
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
1h50FMNPentaerythritol tetranitrate reductase/0.450
1mj9COAHistone acetyltransferase ESA1/0.450
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.450
2iqgF2IBeta-secretase 13.4.23.460.450
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.450
2vkeTACTetracycline repressor protein class D/0.450
3duyAFJBeta-secretase 13.4.23.460.450
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.450
4d89BXDBeta-secretase 13.4.23.460.450
4lcg1WMUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.450
4m83ERYOleandomycin glycosyltransferase2.4.10.450
5a3cNADSIR2 family protein/0.450
1fmlRTLRetinol dehydratase/0.449
1tqf32PBeta-secretase 13.4.23.460.449
2a92NAIL-lactate dehydrogenase/0.449
3a3gDLZLumazine protein/0.449
3toxNAPPutative oxidoreductase/0.449
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.449
4rnuFMNNADPH dehydrogenase 11.6.99.10.449
1h65GDPTranslocase of chloroplast 343.6.50.448
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.448
2abbFMNPentaerythritol tetranitrate reductase/0.448
2bjfDXCCholoylglycine hydrolase3.5.1.240.448
2jb4A14Isopenicillin N synthase1.21.3.10.448
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.448
2y0mACOHistone acetyltransferase KAT8/0.448
3c1y2BADNA integrity scanning protein DisA/0.448
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.448
3owaFADAcyl-CoA dehydrogenase/0.448
3own3OXRenin3.4.23.150.448
3tdj3TJGlutamate receptor 2/0.448
4ambDUDPutative glycosyl transferase/0.448
4egbNADdTDP-glucose 4,6-dehydratase/0.448
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.448
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.447
1i59ANPChemotaxis protein CheA2.7.13.30.447
1mjaCOAHistone acetyltransferase ESA1/0.447
1obnASVIsopenicillin N synthase1.21.3.10.447
1rfuADPPyridoxal kinase2.7.1.350.447
1t2cNAIL-lactate dehydrogenase1.1.1.270.447
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.447
2iko7IGRenin3.4.23.150.447
2iviACWIsopenicillin N synthase1.21.3.10.447
3h06VBPGlutamate receptor 2/0.447
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.447
3v2uATPProtein GAL3/0.447
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
4i6gFADCryptochrome-2/0.447
4lh71X8DNA ligase/0.447
1aa6MGDFormate dehydrogenase H1.1.99.330.446
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.446
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.446
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.446
2d29FADAcyl-CoA dehydrogenase/0.446
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.446
2vwqNAPGlucose 1-dehydrogenase/0.446
3enkUPGUDP-glucose 4-epimerase/0.446
4dbzNDPPutative ketoacyl reductase1.3.10.446
4df2FMNNADPH dehydrogenase/0.446
4e2dFMNDehydrogenase/0.446
4psbGA3Cytokinin-specific binding protein/0.446
4q0kGA3Phytohormone-binding protein/0.446
1b2lNDCAlcohol dehydrogenase1.1.1.10.445
1ds7FMNOxygen-insensitive NAD(P)H nitroreductase/0.445
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.445
1rneC60Renin3.4.23.150.445
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.445
1vbiNADMalate/L-lactate dehydrogenase family protein/0.445
2aa3AP0L-lactate dehydrogenase/0.445
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.445
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.445
2xupTZ5Acetylcholinesterase3.1.1.70.445
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.445
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.445
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.445
4bfvZVVPantothenate kinase2.7.1.330.445
4eo3FMNBacterioferritin comigratory protein/NADH dehydrogenase/0.445
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.445
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.445
1hkuNADC-terminal-binding protein 11.1.10.444
1icpFMN12-oxophytodienoate reductase 11.3.1.420.444
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.444
2il2LIXRenin3.4.23.150.444
3mjrAC2Deoxycytidine kinase2.7.1.740.444
3ziuLSSLeucyl-tRNA synthetase/0.444
4fxy0W2Neurolysin, mitochondrial3.4.24.160.444
4ohwATPProtein clpf-1/0.444
5d3qGDPDynamin-13.6.5.50.444
1jolFFODihydrofolate reductase1.5.1.30.443
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.443
1w6hTITPlasmepsin-23.4.23.390.443
1x8lOXRRetinol dehydratase/0.443
2c20NADUDP-glucose 4-epimerase/0.443
2cv2GSUGlutamate--tRNA ligase6.1.1.170.443
2g1r3IGRenin3.4.23.150.443
2g1y5IGRenin3.4.23.150.443
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.443
2q5g1FAPeroxisome proliferator-activated receptor delta/0.443
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.443
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.443
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.443
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3wv9FEGHmd co-occurring protein HcgE/0.443
4dc0NDPPutative ketoacyl reductase1.3.10.443
4djaFAD(6-4) photolyase/0.443
1rp0AHZThiamine thiazole synthase, chloroplastic/0.442
2npxNADNADH peroxidase1.11.1.10.442
3gegNADShort-chain dehydrogenase/reductase SDR/0.442
4a87NARMajor pollen allergen Bet v 1-A/0.442
4bfxZVXPantothenate kinase2.7.1.330.442
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.442
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.442
7stdCRPScytalone dehydratase4.2.1.940.442
1culFOKAdenylate cyclase type 2/0.441
1culFOKAdenylate cyclase type 5/0.441
1h73ANPHomoserine kinase2.7.1.390.441
1icsFMN12-oxophytodienoate reductase 11.3.1.420.441
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.441
1o9bNAIQuinate/shikimate dehydrogenase/0.441
1x1dSAHC-20 methyltransferase/0.441
2ahrNAPPyrroline-5-carboxylate reductase/0.441
2dvlFADAcyl-CoA dehydrogenase/0.441
2emuSAHDiphthine synthase/0.441
2ft9CHDFatty acid-binding protein 2, liver/0.441
2g226IGRenin3.4.23.150.441
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.441
3h3t16HCollagen type IV alpha-3-binding protein/0.441
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.441
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3vsxR32Renin3.4.23.150.441
3wsjMK1Protease/0.441
4b1rITCTetracycline repressor protein class D/0.441
4e2bFMNDehydrogenase/0.441
4q73FADBifunctional protein PutA/0.441
1f8wFADNADH peroxidase1.11.1.10.440
1gtiGTBGlutathione S-transferase P 12.5.1.180.440
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.440
2hm1LIQBeta-secretase 13.4.23.460.440
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.440
2y60M8FIsopenicillin N synthase1.21.3.10.440
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
3d7kD7KBenzaldehyde lyase/0.440
3d84NDPDihydrofolate reductase1.5.1.30.440
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3fhxPLPPyridoxal kinase2.7.1.350.440
3fktSIIBeta-secretase 13.4.23.460.440
3k5c0BIBeta-secretase 13.4.23.460.440
3oadLPORenin3.4.23.150.440
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.440
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4a81DXCMajor pollen allergen Bet v 1-A/0.440
4a862ANMajor pollen allergen Bet v 1-A/0.440
4b8wNAPGDP-L-fucose synthase1.1.1.2710.440
4lcjNADC-terminal-binding protein 2/0.440
4m9aFDAAcyl-CoA dehydrogenase/0.440
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.440