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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
1kt7RTLRetinol-binding protein 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1kt7RTLRetinol-binding protein 4/1.000
1kt4RTLRetinol-binding protein 4/0.765
1kt6RTLRetinol-binding protein 4/0.671
1iiuRTLRetinol-binding protein 4/0.668
1kt3RTLRetinol-binding protein 4/0.657
1brpRTLRetinol-binding protein 4/0.636
1aqbRTLRetinol-binding protein 4/0.620
1felFENRetinol-binding protein 4/0.602
3fmz2T1Retinol-binding protein 4/0.556
1kt5RTLRetinol-binding protein 4/0.540
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.494
2q9fC3SCholesterol 24-hydroxylase/0.492
1osvCHCBile acid receptor/0.488
1ot7CHCBile acid receptor/0.487
3eq6BCOAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.487
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.486
1lriCLRBeta-elicitin cryptogein/0.484
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.484
4j6cSTRCytochrome P450 monooxygenase/0.481
4echFADPolyamine oxidase FMS1/0.480
1xddAAYIntegrin alpha-L/0.479
2q4wFADCytokinin dehydrogenase 71.5.99.120.479
3tfq07MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.479
3vt8YI3Vitamin D3 receptor/0.479
3ijdC2FMethylenetetrahydrofolate reductase/0.478
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.477
3owaFADAcyl-CoA dehydrogenase/0.477
3r7kFDAProbable acyl CoA dehydrogenase/0.477
2c12FADNitroalkane oxidase1.7.3.10.475
5fm7ADPRuvB-like helicase/0.475
1ot7IU5Bile acid receptor/0.474
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.473
3h6k33TCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.473
3cn8FADPolyamine oxidase FMS1/0.472
3qlrNDPDihydrofolate reductase1.5.1.30.472
4bb3KKAIsopenicillin N synthase1.21.3.10.472
4i421HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.472
1dkfBMSRetinoic acid receptor alpha/0.471
1eioGCHGastrotropin/0.471
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.471
3cndFADPolyamine oxidase FMS1/0.471
3akn11DFatty acid-binding protein, intestinal/0.470
3lu8IQXSerum albumin/0.470
2he5NDPAldo-keto reductase family 1 member C211.1.10.469
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.469
1jraFADFAD-linked sulfhydryl oxidase ERV21.8.3.20.468
4fdnFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.468
4o7uTHFThymidylate synthase/0.468
3p6oETGCamphor 5-monooxygenase1.14.15.10.467
1jq5NADGlycerol dehydrogenase1.1.1.60.466
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.466
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.466
2q5g1FAPeroxisome proliferator-activated receptor delta/0.466
3vs6VSHTyrosine-protein kinase HCK2.7.10.20.466
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.465
2cig1DGDihydrofolate reductase1.5.1.30.465
3bi5FADPolyamine oxidase FMS1/0.465
3h1jSMACytochrome b/0.465
4dggI76Proto-oncogene tyrosine-protein kinase Src2.7.10.20.465
2jn3JN3Fatty acid-binding protein, liver/0.464
3gw9VNILanosterol 14-alpha-demethylase/0.464
3p6nDSOCamphor 5-monooxygenase1.14.15.10.464
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.464
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.464
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.463
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.463
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.463
3qm4PN0Cytochrome P450 2D6/0.463
1hrvSDZGenome polyprotein/0.462
1obnASVIsopenicillin N synthase1.21.3.10.462
2djiFADPyruvate oxidase/0.462
3sdkP3NProteasome subunit beta type-53.4.25.10.461
3sdkP3NProteasome subunit beta type-63.4.25.10.461
1yb5NAPQuinone oxidoreductase1.6.5.50.460
2iltNN1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
4gdpFADPolyamine oxidase FMS1/0.460
4nieNBHNuclear receptor ROR-gamma/0.460
5l3dFADLysine-specific histone demethylase 1A10.460
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.459
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.459
3q71AR6Poly [ADP-ribose] polymerase 142.4.2.300.459
4jbtASDCytochrome P450 monooxygenase/0.459
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.458
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.458
3bhrTHGThymidylate synthase/0.457
3di6PDZGag-Pol polyprotein2.7.7.490.457
4d04FADPhenylacetone monooxygenase1.14.13.920.457
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.457
4pd6URINucleoside permease/0.457
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.456
3mg3ECHOrange carotenoid-binding protein/0.456
3qwbNDPProbable quinone oxidoreductase1.6.5.50.456
3zkyWT4Isopenicillin N synthase1.21.3.10.456
4bj9UHBTankyrase-22.4.2.300.456
4g3jVNTLanosterol 14-alpha-demethylase/0.456
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.455
2jb4A14Isopenicillin N synthase1.21.3.10.455
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.455
3l0lHC3Nuclear receptor ROR-gamma/0.455
3p6pA6BCamphor 5-monooxygenase1.14.15.10.455
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.455
3w8wFADPutative FAD-dependent oxygenase EncM/0.455
4j6bPLOCytochrome P450 monooxygenase/0.455
5eccNAPDehydrofolate reductase type I/0.455
1hb3SCVIsopenicillin N synthase1.21.3.10.454
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.454
1thnADPAnti-sigma F factor/0.454
3d84NDPDihydrofolate reductase1.5.1.30.454
3pfdFDAAcyl-CoA dehydrogenase FadE25/0.454
4i9i1DYTankyrase-12.4.2.300.454
4k4eK4ETankyrase-12.4.2.300.454
4ug2NGIAdenosine receptor A2a/0.454
1tduCB3Thymidylate synthase/0.453
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.453
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.453
2z78H86Geranylgeranyl pyrophosphate synthase/0.453
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.453
5jtbZMAAdenosine receptor A2a/0.453
1dv2ATPBiotin carboxylase6.3.4.140.452
1re9DSOCamphor 5-monooxygenase1.14.15.10.452
2nq8ZIDEnoyl-ACP reductase/0.452
2xw7NDPDihydrofolate reductase/0.452
3bi2FADPolyamine oxidase FMS1/0.452
3vs1VSATyrosine-protein kinase HCK2.7.10.20.452
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.452
4ez8DHFThymidylate synthase2.1.1.450.452
1nkzRG1Light-harvesting protein B-800/850 alpha chain/0.451
1nkzRG1Light-harvesting protein B-800/850 beta chain/0.451
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.451
2c0cNAPProstaglandin reductase 310.451
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.451
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
3v2uATPProtein GAL3/0.451
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.451
4xo7NAPAldo-keto reductase family 1 member C2/0.451
1z6lFADPolyamine oxidase FMS1/0.450
2fznFADBifunctional protein PutA1.5.5.20.450
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2vo7M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3pm9FADPutative oxidoreductase/0.450
4i3vNADAldehyde dehydrogenase (NAD+)/0.450
4qe6JN3Bile acid receptor/0.450
4rpgFADUDP-galactopyranose mutase5.4.99.90.450
4w6z8IDAlcohol dehydrogenase 11.1.1.10.450
5jscFADPutative acyl-CoA dehydrogenase/0.450
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.449
2aibERGBeta-elicitin cinnamomin/0.449
2ebaFADPutative glutaryl-CoA dehydrogenase/0.449
2rm2W43Genome polyprotein/0.449
2x9dITCTetracycline repressor protein class D/0.449
4j6dTESCytochrome P450 monooxygenase/0.449
4q71FADBifunctional protein PutA/0.449
4rupH97Vitamin D3 receptor A/0.449
1poxFADPyruvate oxidase1.2.3.30.448
2belCBOCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
2po7CHDFerrochelatase, mitochondrial4.99.1.10.448
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.448
2xvfFADPutative flavin-containing monooxygenase/0.448
3b8r887Vascular endothelial growth factor receptor 22.7.10.10.448
3ipq965Oxysterols receptor LXR-alpha/0.448
3ol5SAWCamphor 5-monooxygenase1.14.15.10.448
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.448
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.448
4qofFMNRibosyldihydronicotinamide dehydrogenase [quinone]/0.448
5cp8TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
1iyzNDPProbable quinone oxidoreductase/0.447
1xuoLA1Integrin alpha-L/0.447
1ztq033Collagenase 33.4.240.447
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.447
2xviFADPutative flavin-containing monooxygenase/0.447
3gkjHC3Niemann-Pick C1 protein/0.447
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.447
3t8xT8XT-cell surface glycoprotein CD1b/0.447
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4kbyC2EStimulator of interferon genes protein/0.447
4mubOAQSulfotransferase oxamniquine resistance protein/0.447
4s0vSUVOrexin receptor type 2/0.447
2ok7FADFerredoxin--NADP reductase, apicoplast/0.446
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.446
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.446
3uhmRFNUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.446
3up0D7SaceDAF-12/0.446
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.446
4q73FADBifunctional protein PutA/0.446
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.446
1bk0ACVIsopenicillin N synthase1.21.3.10.445
1dg8NDPDihydrofolate reductase1.5.1.30.445
1rd4L08Integrin alpha-L/0.445
1sqi8694-hydroxyphenylpyruvate dioxygenase/0.445
1ykdCMPAdenylate cyclase/0.445
2b3dFADModulator of drug activity B/0.445
2c3qGTXGlutathione S-transferase theta-12.5.1.180.445
2du8FADD-amino-acid oxidase1.4.3.30.445
3e2sFADBifunctional protein PutA1.5.5.20.445
3vtbTKAVitamin D3 receptor/0.445
3w0hW12Vitamin D3 receptor/0.445
4dz5NAPAldo-keto reductase family 1 member C3/0.445
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.445
4xxvNAD3-isopropylmalate dehydrogenase/0.445
1n83CLRNuclear receptor ROR-alpha/0.444
1pr1FMBPurine nucleoside phosphorylase DeoD-type/0.444
1rf9DBRCamphor 5-monooxygenase1.14.15.10.444
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.444
3reoSAH(Iso)eugenol O-methyltransferase2.1.1.1460.444
3wmxNADNAD dependent epimerase/dehydratase/0.444
4fwjFADLysine-specific histone demethylase 1B10.444
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.444
4id71G0Activated CDC42 kinase 1/0.444
4msg2C6Tankyrase-12.4.2.300.444
5dozNDPJamJ/0.444
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.444
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1jscFADAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.443
1n4hREANuclear receptor ROR-beta/0.443
1oc1ASVIsopenicillin N synthase1.21.3.10.443
1q0qNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.443
1v5eFADPyruvate oxidase/0.443
2c0tL3GTyrosine-protein kinase HCK2.7.10.20.443
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.443
2k5tCOAPanD regulatory factor/0.443
2rr1W8RGenome polyprotein/0.443
2yg6FADPutrescine oxidase/0.443
3hdmMMGSerine/threonine-protein kinase Sgk12.7.11.10.443
3lqfNADGalactitol dehydrogenase/0.443
3rhaFDAPutrescine oxidase/0.443
3vt45YIVitamin D3 receptor/0.443
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.443
4at0FADPossible succinate dehydrogenase/0.443
4dpwAGSMevalonate diphosphate decarboxylase/0.443
4iah1DXAlr2278 protein/0.443
4qoeFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.443
4z9g1Q5Corticotropin-releasing factor receptor 1/0.443
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.442
1rx02MCIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.442
1vrwNAIEnoyl-ACP reductase/0.442
2dvlFADAcyl-CoA dehydrogenase/0.442
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.442
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.442
3akm11DFatty acid-binding protein, intestinal/0.442
3jzdNADMaleylacetate reductase/0.442
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.442
4fc00T2Serine/threonine-protein kinase B-raf2.7.11.10.442
4g20484Vitamin D3 receptor A/0.442
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.442
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.442
4li81XQTankyrase-12.4.2.300.442
5k2bZMAAdenosine receptor A2a/0.442
3sn6P0GBeta-2 adrenergic receptor/0.442
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.441
1geuNADGlutathione reductase1.8.1.70.441
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1tysDHFThymidylate synthase/0.441
1uyfPU1Heat shock protein HSP 90-alpha/0.441
2d4eNAD5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenaseiheyensis HTE831]/0.441
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.441
2qfxNDPIsocitrate dehydrogenase [NADP], mitochondrial1.1.1.420.441
2uxwTH3Very long-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.90.441
2uxxFAJLysine-specific histone demethylase 1A10.441
3cntFADPolyamine oxidase FMS1/0.441
3is9AC7Gag-Pol polyprotein2.7.7.490.441
3m0oFADMonomeric sarcosine oxidase1.5.3.10.441
3rpnGTXGlutathione S-transferase kappa 12.5.1.180.441
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.441
3zlnH0YBcl-2-like protein 1/0.441
4dbs0HVAldo-keto reductase family 1 member C3/0.441
4ijrNDPD-arabinose dehydrogenase [NAD(P)+] heavy chain1.1.1.1170.441
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
5ifyUMPGlucose-1-phosphate thymidylyltransferase/0.441
1kqoDNDNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.440
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.440
1m13HYFNuclear receptor subfamily 1 group I member 2/0.440
1p8dCO1Oxysterols receptor LXR-beta/0.440
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.440
1qorNDPQuinone oxidoreductase 1/0.440
1s1pNAPAldo-keto reductase family 1 member C3/0.440
2c0iL1GTyrosine-protein kinase HCK2.7.10.20.440
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.440
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
3bbtFMMReceptor tyrosine-protein kinase erbB-42.7.10.10.440
3i0rRT3Gag-Pol polyprotein2.7.7.490.440
3vrvYSDVitamin D3 receptor/0.440
4a7b3W4Collagenase 33.4.240.440
4b1fKRHGlutamate racemase/0.440
4d03NAPPhenylacetone monooxygenase1.14.13.920.440
4iacACPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
4ib4ERM5-hydroxytryptamine receptor 2B/0.440
4jq3NAPAldo-keto reductase family 1 member C2/0.440