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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
4kouC04Uncharacterized protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4kouC04Uncharacterized protein/1.000
4kos4KOUncharacterized protein/0.698
4kotCE3Uncharacterized protein/0.694
4koyCSCUncharacterized protein/0.681
4koxCLSUncharacterized protein/0.638
4kovKOVUncharacterized protein/0.633
4kowCFXUncharacterized protein/0.617
4klvKLVUncharacterized protein/0.597
2jb4A14Isopenicillin N synthase1.21.3.10.499
4lzwTHMUridine phosphorylase/0.496
1ve3SAMUncharacterized protein/0.495
1dr2TAPDihydrofolate reductase1.5.1.30.491
1obnASVIsopenicillin N synthase1.21.3.10.491
4zu44TGWxcM-like protein/0.489
1blzACVIsopenicillin N synthase1.21.3.10.488
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.486
1qiqACCIsopenicillin N synthase1.21.3.10.485
1u1d181Uridine phosphorylase2.4.2.30.485
1bk0ACVIsopenicillin N synthase1.21.3.10.483
3zoiM2WIsopenicillin N synthase1.21.3.10.481
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.480
4iji99TGlutathione S-transferase-like protein YibF/0.480
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.480
2vbdV10Isopenicillin N synthase1.21.3.10.478
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.478
4fxfATPPyruvate kinase PKM2.7.1.400.477
4cdmFO1Deoxyribodipyrimidine photolyase/0.476
2iviACWIsopenicillin N synthase1.21.3.10.475
2y6fM9FIsopenicillin N synthase1.21.3.10.474
1hb1OCVIsopenicillin N synthase1.21.3.10.473
1pqc444Oxysterols receptor LXR-beta/0.473
2y60M8FIsopenicillin N synthase1.21.3.10.473
3bi6396Wee1-like protein kinase2.7.10.20.473
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
3atzFMNProstaglandin F2a synthase/0.472
1vgqCAOFormyl-CoA:oxalate CoA-transferase/0.470
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.470
3p62FMNPentaerythritol tetranitrate reductase/0.469
4uugPXGBranched-chain amino acid aminotransferase, putative/0.469
1qjfACSIsopenicillin N synthase1.21.3.10.468
1u1f183Uridine phosphorylase2.4.2.30.468
3arvSAUChitinase A/0.468
3junAKDPhenazine biosynthesis protein A/B/0.468
4fcr0TMHeat shock protein HSP 90-alpha/0.468
1hb3SCVIsopenicillin N synthase1.21.3.10.467
1oc1ASVIsopenicillin N synthase1.21.3.10.467
4abzT1CTetracycline repressor protein class D/0.464
1nbiSAMGlycine N-methyltransferase2.1.1.200.463
2bgjFADNADPH:ferredoxin reductase/0.463
2bsxNOSPurine nucleoside phosphorylase/0.463
1u1gBBBUridine phosphorylase2.4.2.30.462
1zgv501Prothrombin3.4.21.50.462
2zf051UProthrombin3.4.21.50.462
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4a81DXCMajor pollen allergen Bet v 1-A/0.462
4ol0GTPGTP-binding nuclear protein Ran/0.462
1ascNPLAspartate aminotransferase2.6.1.10.461
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.461
3ksqZ96Protein farnesyltransferase subunit beta2.5.1.580.461
3ox4NADAlcohol dehydrogenase 21.1.1.10.461
3w0gW07Vitamin D3 receptor/0.461
2o7pNAPRiboflavin biosynthesis protein RibD/0.460
2vbpVB1Isopenicillin N synthase1.21.3.10.460
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.459
2bu9HFVIsopenicillin N synthase1.21.3.10.458
3cneFMNPutative protease I/0.458
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.458
2aclL05Oxysterols receptor LXR-alpha/0.457
2xpwOTCTetracycline repressor protein class D/0.457
2znk31UProthrombin3.4.21.50.457
1d6w00RProthrombin3.4.21.50.456
2vn1FK5Peptidylprolyl isomerase/0.456
3zkyWT4Isopenicillin N synthase1.21.3.10.456
1uzwCDHIsopenicillin N synthase1.21.3.10.455
3lz6A0DCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.455
3rsv3RSBeta-secretase 13.4.23.460.455
4oztP1AEcdysone receptor, putative/0.455
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.455
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.454
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.454
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.454
4kbyC2EStimulator of interferon genes protein/0.454
4o2rGDPGTP-binding protein Rheb/0.454
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.453
2vqoTFGHistone deacetylase 43.5.1.980.453
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.453
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.453
3v2uATPProtein GAL3/0.453
3wtkTH4Acetylcholine-binding protein/0.453
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.453
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.453
1vgrCOAFormyl-CoA:oxalate CoA-transferase/0.452
2gd2CAAProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.452
2pksG44Prothrombin3.4.21.50.452
2wo7ASVIsopenicillin N synthase1.21.3.10.452
3crzFADFerredoxin--NADP+ reductase/0.452
3wleNAD(R)-specific carbonyl reductase/0.452
2eixFADNADH-cytochrome b5 reductase/0.451
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.451
2zc922UProthrombin3.4.21.50.451
3akn11DFatty acid-binding protein, intestinal/0.451
3eufBAUUridine phosphorylase 1/0.451
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.451
4eb5PLPCysteine desulfurase IscS 2/0.451
1q3gUDAUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.450
2v59LZKBiotin carboxylase6.3.4.140.450
2zg050UProthrombin3.4.21.50.450
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.450
3qs817DAnthranilate phosphoribosyltransferase/0.450
3qt62P0Mevalonate diphosphate decarboxylase/0.450
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.450
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.450
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.450
4jx1CAMCamphor 5-monooxygenase1.14.15.10.450
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.450
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.450
2a9z26AAdenosine kinase2.7.1.200.449
2bgiFADNADPH:ferredoxin reductase/0.449
2gjlFMNNitronate monooxygenase1.13.12.160.449
3f3sNADLambda-crystallin homolog/0.449
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.449
3l0lHC3Nuclear receptor ROR-gamma/0.449
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.449
4locBTNPyruvate carboxylase/0.449
5fm7ADPRuvB-like helicase/0.449
1cqp803Integrin alpha-L/0.448
1mv8GDXGDP-mannose 6-dehydrogenase1.1.1.1320.448
1vyrFMNPentaerythritol tetranitrate reductase/0.448
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.448
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3ekuCY9Actin-5C/0.448
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.448
3tm5SFGUncharacterized protein/0.448
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.448
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.448
4jx1CAHCamphor 5-monooxygenase1.14.15.10.448
1p93DEXGlucocorticoid receptor/0.447
1pq944BOxysterols receptor LXR-beta/0.447
1sirNBCGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.447
1udaUFGUDP-glucose 4-epimerase5.1.3.20.447
2hg1N5OEndoplasmin/0.447
2rlcCHDCholoylglycine hydrolase3.5.1.240.447
2xvfFADPutative flavin-containing monooxygenase/0.447
3ha5SFGHydroxymycolate synthase MmaA42.1.10.447
3hl0NADMaleylacetate reductase/0.447
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.447
3qwbNDPProbable quinone oxidoreductase1.6.5.50.447
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.447
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.447
1mu6CDAProthrombin3.4.21.50.446
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
1r2jFADFkbI/0.446
1wuaAP8Actin, alpha skeletal muscle/0.446
2zcvNDPQuinone oxidoreductase 21.6.5.20.446
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.446
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.446
5dw50T1Succinyl-CoA:acetate CoA-transferase/0.446
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.446
2o7oDXTTetracycline repressor protein class D/0.445
2r8oT5XTransketolase 1/0.445
2zhe13UProthrombin3.4.21.50.445
3eksCY9Actin-5C/0.445
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.445
3h5sH5SGenome polyprotein2.7.7.480.445
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.445
3v0p4GWHisto-blood group ABO system transferase/0.445
4i13FOLDihydrofolate reductase1.5.1.30.445
4l2xYL2Farnesyl pyrophosphate synthase2.5.1.100.445
5fd8A5APutative carboxypeptidase yocD/0.445
1n08ADPRiboflavin kinase2.7.1.260.444
1w06W05Isopenicillin N synthase1.21.3.10.444
2fk8SAMHydroxymycolate synthase MmaA42.1.10.444
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.444
2z9dFMNFMN-dependent NADH-azoreductase/0.444
3cib314Beta-secretase 13.4.23.460.444
3eq02TSProthrombin3.4.21.50.444
4b68NAPL-ornithine N(5)-monooxygenase/0.444
4mv8ACPBiotin carboxylase6.3.4.140.444
5c2tFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.444
1icpFMN12-oxophytodienoate reductase 11.3.1.420.443
1t5bFMNFMN-dependent NADH-azoreductase/0.443
1thyUMPThymidylate synthase/0.443
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.443
2gvdFKPAdenylate cyclase type 2/0.443
2gvdFKPAdenylate cyclase type 5/0.443
2zfq45UProthrombin3.4.21.50.443
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
4auxXTCTetracycline repressor protein class D/0.443
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.443
4psbGA3Cytokinin-specific binding protein/0.443
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.442
2b03TUDPhospholipase A2, major isoenzyme3.1.1.40.442
2cjfRP43-dehydroquinate dehydratase4.2.1.100.442
2fs4PZ1Renin3.4.23.150.442
2h63NAPBiliverdin reductase A1.3.1.240.442
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.442
2uxoTACHTH-type transcriptional regulator TtgR/0.442
2vnkFADNADPH:ferredoxin reductase/0.442
2y3sTIRTamL/0.442
3h0bB35Beta-secretase 13.4.23.460.442
3rlq3RQHeat shock protein HSP 90-alpha/0.442
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
3up0D7SaceDAF-12/0.442
3w0c6DSVitamin D3 receptor/0.442
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.442
4bfxZVXPantothenate kinase2.7.1.330.442
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.442
4e2yJHZMethyltransferase/0.442
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.442
4wctFADFructosyl amine:oxygen oxidoreductase/0.442
1a8pFADFerredoxin--NADP reductase/0.441
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.441
1mzcBNEProtein farnesyltransferase subunit beta2.5.1.580.441
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.441
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.441
1oytFSNProthrombin3.4.21.50.441
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.441
1xh6R94cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
1zgi382Prothrombin3.4.21.50.441
2jgsBTNAvidin/0.441
2vjmCOAFormyl-CoA:oxalate CoA-transferase/0.441
2zgx29UProthrombin3.4.21.50.441
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3rpeFADPutative modulator of drug activity/0.441
4do30LAFatty-acid amide hydrolase 13.5.1.990.441
4egbNADdTDP-glucose 4,6-dehydratase/0.441
4jtrIZPAldo-keto reductase family 1 member C2/0.441
4jzr4JREgl nine homolog 1/0.441
4lol1YEStimulator of interferon genes protein/0.441
1afeALZProthrombin3.4.21.50.440
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.440
1qd1FONFormimidoyltransferase-cyclodeaminase2.1.2.50.440
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.440
2eniSAHDiphthine synthase/0.440
2jih097A disintegrin and metalloproteinase with thrombospondin motifs 13.4.240.440
3jzdNADMaleylacetate reductase/0.440
3q43D66M1 family aminopeptidase3.4.110.440
4b63NAPL-ornithine N(5)-monooxygenase/0.440
4udaDEXMineralocorticoid receptor/0.440
4yjdFADD-amino-acid oxidase1.4.3.30.440
5stdUNNScytalone dehydratase4.2.1.940.440
6ctsCICCitrate synthase, mitochondrial2.3.3.10.440
3sn6P0GBeta-2 adrenergic receptor/0.440