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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
1kt4RTLRetinol-binding protein 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1kt4RTLRetinol-binding protein 4/1.000
1kt7RTLRetinol-binding protein 4/0.762
1kt3RTLRetinol-binding protein 4/0.675
1aqbRTLRetinol-binding protein 4/0.666
1kt6RTLRetinol-binding protein 4/0.649
1iiuRTLRetinol-binding protein 4/0.637
1felFENRetinol-binding protein 4/0.608
1brpRTLRetinol-binding protein 4/0.603
3fmz2T1Retinol-binding protein 4/0.541
1osvCHCBile acid receptor/0.508
2q9fC3SCholesterol 24-hydroxylase/0.505
1kt5RTLRetinol-binding protein 4/0.504
4j6cSTRCytochrome P450 monooxygenase/0.501
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.499
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.492
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.492
3p6oETGCamphor 5-monooxygenase1.14.15.10.487
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.480
3eq6BCOAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.480
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.478
4nieNBHNuclear receptor ROR-gamma/0.477
3bi5FADPolyamine oxidase FMS1/0.476
4j6dTESCytochrome P450 monooxygenase/0.476
1nkzRG1Light-harvesting protein B-800/850 alpha chain/0.475
1nkzRG1Light-harvesting protein B-800/850 beta chain/0.475
1sqi8694-hydroxyphenylpyruvate dioxygenase/0.475
4dggI76Proto-oncogene tyrosine-protein kinase Src2.7.10.20.474
1hrvSDZGenome polyprotein/0.473
1lriCLRBeta-elicitin cryptogein/0.473
1ot7CHCBile acid receptor/0.473
2q4wFADCytokinin dehydrogenase 71.5.99.120.472
3own3OWRenin3.4.23.150.471
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.471
2qa2FADPolyketide oxygenase CabE/0.470
2qu6857Vascular endothelial growth factor receptor 22.7.10.10.469
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.469
4ez8DHFThymidylate synthase2.1.1.450.469
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.468
2iltNN1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.467
3bhrTHGThymidylate synthase/0.467
3vs6VSHTyrosine-protein kinase HCK2.7.10.20.467
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.466
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.466
3h6k33TCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.466
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.466
1xuoLA1Integrin alpha-L/0.465
3vt8YI3Vitamin D3 receptor/0.465
3h1jSMACytochrome b/0.464
4i3vNADAldehyde dehydrogenase (NAD+)/0.464
1yb5NAPQuinone oxidoreductase1.6.5.50.463
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.463
4g3jVNTLanosterol 14-alpha-demethylase/0.463
4ocvANPAminoglycoside phosphotransferase/0.463
3p6nDSOCamphor 5-monooxygenase1.14.15.10.462
4kaoKAOFocal adhesion kinase 12.7.10.20.462
4li71XPTankyrase-12.4.2.300.462
1tysDHFThymidylate synthase/0.461
3owaFADAcyl-CoA dehydrogenase/0.461
4jbtASDCytochrome P450 monooxygenase/0.461
3d3eD3ECorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
3lu8IQXSerum albumin/0.460
4d04FADPhenylacetone monooxygenase1.14.13.920.460
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.459
2he5NDPAldo-keto reductase family 1 member C211.1.10.459
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.459
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.459
3ox4NADAlcohol dehydrogenase 21.1.1.10.459
2c0cNAPProstaglandin reductase 310.458
2r04W71Genome polyprotein/0.458
3u1y03IUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.458
4at0FADPossible succinate dehydrogenase/0.458
1bxoPP7Penicillopepsin-13.4.23.200.457
3nalDBKCalcium-transporting ATPase/0.457
4cnjFADL-amino acid oxidase/0.457
4echFADPolyamine oxidase FMS1/0.457
1eioGCHGastrotropin/0.456
1ey3DAKEnoyl-CoA hydratase, mitochondrial4.2.1.170.456
1ot7IU5Bile acid receptor/0.456
1yhjR6CPyridoxal kinase2.7.1.350.456
3p6pA6BCamphor 5-monooxygenase1.14.15.10.456
4d03NAPPhenylacetone monooxygenase1.14.13.920.456
1tj0FADBifunctional protein PutA1.5.5.20.455
3ce31FNHepatocyte growth factor receptor2.7.10.10.455
3gw9VNILanosterol 14-alpha-demethylase/0.455
3p3zP3ZPutative cytochrome P450/0.455
4gdpFADPolyamine oxidase FMS1/0.455
4j6bPLOCytochrome P450 monooxygenase/0.455
4k4eK4ETankyrase-12.4.2.300.455
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
6ctsCICCitrate synthase, mitochondrial2.3.3.10.455
1geuNADGlutathione reductase1.8.1.70.454
1iepSTITyrosine-protein kinase ABL12.7.10.20.454
1ppm0P1Penicillopepsin-13.4.23.200.454
3b6zCO7Enoyl reductase LovC10.454
4ia7BIVVitamin D3 receptor A/0.454
4jtqNAPAldo-keto reductase family 1 member C2/0.454
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.453
3abaFLICytochrome P450/0.453
3icrCOACoenzyme A disulfide reductase/0.453
3q71AR6Poly [ADP-ribose] polymerase 142.4.2.300.453
3sfi3SFHTH-type transcriptional regulator EthR/0.453
4dbs0HVAldo-keto reductase family 1 member C3/0.453
4iacACPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.453
5fm7ADPRuvB-like helicase/0.453
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.452
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
2qfxNDPIsocitrate dehydrogenase [NADP], mitochondrial1.1.1.420.452
3dtwA96Vascular endothelial growth factor receptor 22.7.10.10.452
3h86AP5Adenylate kinase/0.452
3vs0VS0Tyrosine-protein kinase HCK2.7.10.20.452
4li81XQTankyrase-12.4.2.300.452
1jraFADFAD-linked sulfhydryl oxidase ERV21.8.3.20.451
1rrmAPRLactaldehyde reductase1.1.1.770.451
2dw4FADLysine-specific histone demethylase 1A10.451
2g263LGRenin3.4.23.150.451
3cndFADPolyamine oxidase FMS1/0.451
3di6PDZGag-Pol polyprotein2.7.7.490.451
4a95NHWGlycylpeptide N-tetradecanoyltransferase/0.451
4bb3KKAIsopenicillin N synthase1.21.3.10.451
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.451
4mt92D6Tankyrase-12.4.2.300.451
4ysjADPCalmodulin-like domain protein kinase/0.451
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.451
1n83CLRNuclear receptor ROR-alpha/0.450
2d4eNAD5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenaseiheyensis HTE831]/0.450
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.450
2uxxFAJLysine-specific histone demethylase 1A10.450
2wleCOAPolysialic acid O-acetyltransferase/0.450
2zb8IMNProstaglandin reductase 21.3.1.480.450
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3ju8NADN-succinylglutamate 5-semialdehyde dehydrogenase1.2.1.710.450
3o96IQORAC-alpha serine/threonine-protein kinase2.7.11.10.450
3w0hW12Vitamin D3 receptor/0.450
4a7b3W4Collagenase 33.4.240.450
4bj9UHBTankyrase-22.4.2.300.450
4ejn0R4RAC-alpha serine/threonine-protein kinase2.7.11.10.450
2c12FADNitroalkane oxidase1.7.3.10.449
2j3kNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.449
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.449
3bhlTHGThymidylate synthase/0.449
3cp9C19Vascular endothelial growth factor receptor 22.7.10.10.449
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
3qm4PN0Cytochrome P450 2D6/0.449
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.449
4fdnFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.449
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.449
4oh4ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.449
1trgCB3Thymidylate synthase/0.448
1v5eFADPyruvate oxidase/0.448
2dubCO8Enoyl-CoA hydratase, mitochondrial4.2.1.170.448
3imxB84Glucokinase2.7.1.20.448
5ag7MYAGlycylpeptide N-tetradecanoyltransferase/0.448
5jtbZMAAdenosine receptor A2a/0.448
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.447
2rr1W8RGenome polyprotein/0.447
3mg3ECHOrange carotenoid-binding protein/0.447
3wmxNADNAD dependent epimerase/dehydratase/0.447
4i9i1DYTankyrase-12.4.2.300.447
4ia2BIVVitamin D3 receptor A/0.447
4iarERM5-hydroxytryptamine receptor 1B/0.447
3sn6P0GBeta-2 adrenergic receptor/0.447
1hb1OCVIsopenicillin N synthase1.21.3.10.446
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.446
3p6mDSOCamphor 5-monooxygenase1.14.15.10.446
3thrC2FGlycine N-methyltransferase2.1.1.200.446
4dz5NAPAldo-keto reductase family 1 member C3/0.446
4gapNADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.446
4iqqD16Thymidylate synthase/0.446
1qiqACCIsopenicillin N synthase1.21.3.10.445
1ztq033Collagenase 33.4.240.445
2jn3JN3Fatty acid-binding protein, liver/0.445
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
2z4w749Geranylgeranyl pyrophosphate synthase/0.445
2zb3NDPProstaglandin reductase 21.3.1.480.445
3ds6A17Mitogen-activated protein kinase 14/0.445
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
3icsCOACoenzyme A disulfide reductase/0.445
3vnt0JAVascular endothelial growth factor receptor 22.7.10.10.445
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.445
4iah1DXAlr2278 protein/0.445
4iaq2GM5-hydroxytryptamine receptor 1B/0.445
4ug2NGIAdenosine receptor A2a/0.445
2bktRPFRenin3.4.23.150.444
2c3qGTXGlutathione S-transferase theta-12.5.1.180.444
2cig1DGDihydrofolate reductase1.5.1.30.444
2e48FADD-amino-acid oxidase1.4.3.30.444
2fhjMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.444
2k5tCOAPanD regulatory factor/0.444
2w98P1ZProstaglandin reductase 21.3.1.480.444
3ijdC2FMethylenetetrahydrofolate reductase/0.444
3mlaJJZProbable nicotinate-nucleotide adenylyltransferase/0.444
3tmz06XCytochrome P450 2B41.14.14.10.444
4b13NHWGlycylpeptide N-tetradecanoyltransferase/0.444
4j2wFADKynurenine 3-monooxygenase/0.444
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.444
4kqqVPPPeptidoglycan D,D-transpeptidase FtsI/0.444
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.444
5ig2NADShort-chain dehydrogenase/reductase SDR/0.444
1oc1ASVIsopenicillin N synthase1.21.3.10.443
2belCBOCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
3deiRXBCaspase-33.4.22.560.443
3hng8STVascular endothelial growth factor receptor 12.7.10.10.443
3pm9FADPutative oxidoreductase/0.443
3vtbTKAVitamin D3 receptor/0.443
4isk1JYThymidylate synthase/0.443
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.443
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
2hyySTITyrosine-protein kinase ABL12.7.10.20.442
2yjxYJXHeat shock protein HSP 90-alpha/0.442
3ol5SAWCamphor 5-monooxygenase1.14.15.10.442
3zkyWT4Isopenicillin N synthase1.21.3.10.442
4bfpSWYTankyrase-22.4.2.300.442
4i421HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.442
4jtz1NWGenome polyprotein2.7.7.480.442
4lva20MNicotinamide phosphoribosyltransferase2.4.2.120.442
4o8aFADBifunctional protein PutA1.2.1.880.442
5l3dFADLysine-specific histone demethylase 1A10.442
1jq5NADGlycerol dehydrogenase1.1.1.60.441
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.441
1re9DSOCamphor 5-monooxygenase1.14.15.10.441
1t0lNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.441
2djiFADPyruvate oxidase/0.441
2hdjNDPAldo-keto reductase family 1 member C2/0.441
2v5xV5XHistone deacetylase 83.5.1.980.441
3f5p741Insulin-like growth factor 1 receptor2.7.10.10.441
3is9AC7Gag-Pol polyprotein2.7.7.490.441
3k4nFADPyranose 2-oxidase/0.441
3kytHC2Nuclear receptor ROR-gamma/0.441
3sdkP3NProteasome subunit beta type-53.4.25.10.441
3sdkP3NProteasome subunit beta type-63.4.25.10.441
3zos0LIEpithelial discoidin domain-containing receptor 12.7.10.10.441
4i3zADPCyclin-dependent kinase 22.7.11.220.441
1hb3SCVIsopenicillin N synthase1.21.3.10.440
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.440
2aibERGBeta-elicitin cinnamomin/0.440
2c0iL1GTyrosine-protein kinase HCK2.7.10.20.440
2ebaFADPutative glutaryl-CoA dehydrogenase/0.440
2f7e2EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2oa1FADFlavin-dependent tryptophan halogenase RebH1.14.19.90.440
2p15EZTEstrogen receptor/0.440
3apyFADMethylenetetrahydrofolate reductase/0.440
3b8q900Vascular endothelial growth factor receptor 22.7.10.10.440
3qrwNDPPutative ketoacyl reductase1.3.10.440
3w2wATPCRISPR system Cmr subunit Cmr2/0.440
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.440
4a2zMYAGlycylpeptide N-tetradecanoyltransferase/0.440
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.440
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.440
4ockANPN-acetylhexosamine 1-kinase2.7.1.1620.440