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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
1kt6RTLRetinol-binding protein 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1kt6RTLRetinol-binding protein 4/1.000
1kt3RTLRetinol-binding protein 4/0.692
1kt7RTLRetinol-binding protein 4/0.683
1kt4RTLRetinol-binding protein 4/0.644
1aqbRTLRetinol-binding protein 4/0.607
1felFENRetinol-binding protein 4/0.597
1brpRTLRetinol-binding protein 4/0.589
1iiuRTLRetinol-binding protein 4/0.585
3fmz2T1Retinol-binding protein 4/0.519
1osvCHCBile acid receptor/0.515
1kt5RTLRetinol-binding protein 4/0.509
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.500
2zynBCDPeriplasmic binding protein/0.491
5fm7ADPRuvB-like helicase/0.489
3h1jSMACytochrome b/0.488
4kl9NDPDihydrofolate reductase1.5.1.30.488
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.482
4s0vSUVOrexin receptor type 2/0.480
3sn6P0GBeta-2 adrenergic receptor/0.479
1lriCLRBeta-elicitin cryptogein/0.478
1thnADPAnti-sigma F factor/0.478
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.476
2cig1DGDihydrofolate reductase1.5.1.30.476
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.474
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.474
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.471
3c3xNAPEugenol synthase 11.1.1.3180.471
1xddAAYIntegrin alpha-L/0.470
3eq6BCOAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.470
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.470
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.470
2xpwOTCTetracycline repressor protein class D/0.469
4a7b3W4Collagenase 33.4.240.469
4j6cSTRCytochrome P450 monooxygenase/0.469
4jdaA9SAbscisic acid receptor PYL3/0.469
1xuoLA1Integrin alpha-L/0.468
3qlrNDPDihydrofolate reductase1.5.1.30.468
3w8wFADPutative FAD-dependent oxygenase EncM/0.467
2aviBTNAvidin/0.465
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.465
3sdkP3NProteasome subunit beta type-53.4.25.10.465
3sdkP3NProteasome subunit beta type-63.4.25.10.465
4j6dTESCytochrome P450 monooxygenase/0.465
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
2q4wFADCytokinin dehydrogenase 71.5.99.120.464
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.463
3kpzZNEVitamin D3 receptor/0.463
3wthIM4Acetylcholine-binding protein/0.463
4echFADPolyamine oxidase FMS1/0.463
4jbtASDCytochrome P450 monooxygenase/0.463
1rd4L08Integrin alpha-L/0.462
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.462
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.462
1fm4DXCMajor pollen allergen Bet v 1-L/0.461
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.461
4dggI76Proto-oncogene tyrosine-protein kinase Src2.7.10.20.461
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.460
1hdoNAPFlavin reductase (NADPH)/0.459
4q71FADBifunctional protein PutA/0.459
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.459
1db1VDXVitamin D3 receptor/0.458
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
2q9fC3SCholesterol 24-hydroxylase/0.458
2xw7NDPDihydrofolate reductase/0.458
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.458
1fwmCB3Thymidylate synthase/0.457
1ie8KH1Vitamin D3 receptor/0.457
2iltNN1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.457
3cn8FADPolyamine oxidase FMS1/0.457
4d04FADPhenylacetone monooxygenase1.14.13.920.457
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.457
4qe6JN3Bile acid receptor/0.457
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.456
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
3phiNDPShikimate dehydrogenase (NADP(+))/0.456
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.456
4j6bPLOCytochrome P450 monooxygenase/0.456
2rkvZBATrichothecene 3-O-acetyltransferase/0.455
3b6zCO7Enoyl reductase LovC10.455
3lanKBTGag-Pol polyprotein2.7.7.490.455
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.455
3vs6VSHTyrosine-protein kinase HCK2.7.10.20.455
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.455
4bj9UHBTankyrase-22.4.2.300.455
1ot7IU5Bile acid receptor/0.454
2nnhREACytochrome P450 2C8/0.454
2uxoTACHTH-type transcriptional regulator TtgR/0.454
2vo7M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
4dz5NAPAldo-keto reductase family 1 member C3/0.454
4gdpFADPolyamine oxidase FMS1/0.454
4i3zADPCyclin-dependent kinase 22.7.11.220.454
5jscFADPutative acyl-CoA dehydrogenase/0.454
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.453
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.453
2c3qGTXGlutathione S-transferase theta-12.5.1.180.453
2dvlFADAcyl-CoA dehydrogenase/0.453
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.453
2he5NDPAldo-keto reductase family 1 member C211.1.10.453
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.453
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
2x9dITCTetracycline repressor protein class D/0.453
3dleGFAGag-Pol polyprotein2.7.7.490.453
3w0gW07Vitamin D3 receptor/0.453
4ly91YYGlucokinase regulatory protein/0.453
4nieNBHNuclear receptor ROR-gamma/0.453
4pd6URINucleoside permease/0.453
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3gw9VNILanosterol 14-alpha-demethylase/0.452
3k4nFADPyranose 2-oxidase/0.452
3p6pA6BCamphor 5-monooxygenase1.14.15.10.452
3uteFADUDP-galactopyranose mutase/0.452
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.452
4qoeFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.452
1zeoC01Peroxisome proliferator-activated receptor gamma/0.451
3a3yOBNSodium/potassium-transporting ATPase subunit alpha/0.451
3bi5FADPolyamine oxidase FMS1/0.451
3d84NDPDihydrofolate reductase1.5.1.30.451
3ezpB3NHistone deacetylase 83.5.1.980.451
3up0D7SaceDAF-12/0.451
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.451
1hb3SCVIsopenicillin N synthase1.21.3.10.450
1ykdCMPAdenylate cyclase/0.450
3di6PDZGag-Pol polyprotein2.7.7.490.450
3lu8IQXSerum albumin/0.450
4gl4NAIAlcohol dehydrogenase class-3/0.450
4ipw1G7Mycocyclosin synthase1.14.21.90.450
4jq3NAPAldo-keto reductase family 1 member C2/0.450
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.449
1dg8NDPDihydrofolate reductase1.5.1.30.449
1eioGCHGastrotropin/0.449
1ie9VDXVitamin D3 receptor/0.449
2f7e2EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
2nq8ZIDEnoyl-ACP reductase/0.449
2o4rVD5Vitamin D3 receptor/0.449
3vrvYSDVitamin D3 receptor/0.449
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.449
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.449
5fklTDCTetracycline repressor protein class D/0.449
1cf3FADGlucose oxidase1.1.3.40.448
1hvyD16Thymidylate synthase2.1.1.450.448
1xajNAD3-dehydroquinate synthase/0.448
1z6lFADPolyamine oxidase FMS1/0.448
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.448
2trtTACTetracycline repressor protein class D/0.448
2ycfYCFSerine/threonine-protein kinase Chk22.7.11.10.448
3w5p4OAVitamin D3 receptor/0.448
4auxXTCTetracycline repressor protein class D/0.448
4jx1CAHCamphor 5-monooxygenase1.14.15.10.448
1hb1OCVIsopenicillin N synthase1.21.3.10.447
2c4iBTNAvidin/0.447
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.447
2zymACXPeriplasmic binding protein/0.447
3el8PD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.447
3ox4NADAlcohol dehydrogenase 21.1.1.10.447
3vt5YI2Vitamin D3 receptor/0.447
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.447
4iawLIZNeutrophil gelatinase-associated lipocalin/0.447
4knzCB3Thymidylate synthase/0.447
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.446
1lluNADAlcohol dehydrogenase/0.446
1tysDHFThymidylate synthase/0.446
2d29FADAcyl-CoA dehydrogenase/0.446
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.446
2hkoFADLysine-specific histone demethylase 1A10.446
2igoFADPyranose 2-oxidase/0.446
2jn3JN3Fatty acid-binding protein, liver/0.446
2k5tCOAPanD regulatory factor/0.446
2vqbFADPutative flavin-containing monooxygenase/0.446
2z78H86Geranylgeranyl pyrophosphate synthase/0.446
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.446
3p9tTCLRepressor/0.446
3tfq07MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.446
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.446
5a3cNADSIR2 family protein/0.446
5cp8TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
1dv2ATPBiotin carboxylase6.3.4.140.445
2xvfFADPutative flavin-containing monooxygenase/0.445
3q71AR6Poly [ADP-ribose] polymerase 142.4.2.300.445
3uoyNAP2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.445
3vt8YI3Vitamin D3 receptor/0.445
4xq9NADHomospermidine synthase2.5.1.440.445
1bk0ACVIsopenicillin N synthase1.21.3.10.444
1ma0NADAlcohol dehydrogenase class-31.1.1.10.444
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.444
1vbnYSATyrosine--tRNA ligase6.1.1.10.444
1xzqFONtRNA modification GTPase MnmE3.6.50.444
2bktRPFRenin3.4.23.150.444
2dw4FADLysine-specific histone demethylase 1A10.444
2rr1W8RGenome polyprotein/0.444
2ydxNAPMethionine adenosyltransferase 2 subunit beta/0.444
3bgxMEFThymidylate synthase/0.444
3h6k33TCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
3ihgFADAklavinone 12-hydroxylase RdmE/0.444
3m0oFADMonomeric sarcosine oxidase1.5.3.10.444
3vt65YIVitamin D3 receptor/0.444
4g3jVNTLanosterol 14-alpha-demethylase/0.444
4q73FADBifunctional protein PutA/0.444
4xxvNAD3-isopropylmalate dehydrogenase/0.444
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.444
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.443
2ykbYKBHeat shock protein HSP 90-alpha/0.443
3cndFADPolyamine oxidase FMS1/0.443
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.443
3qwbNDPProbable quinone oxidoreductase1.6.5.50.443
4b1rITCTetracycline repressor protein class D/0.443
4qzuRTLRetinol-binding protein 2/0.443
4yt5H4MH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338/0.443
1cqp803Integrin alpha-L/0.442
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.442
1iyzNDPProbable quinone oxidoreductase/0.442
1q6nP90Tyrosine-protein phosphatase non-receptor type 13.1.3.480.442
1ztq033Collagenase 33.4.240.442
2c0cNAPProstaglandin reductase 310.442
2pswCOAN-alpha-acetyltransferase 50/0.442
2xlrNAPPutative flavin-containing monooxygenase/0.442
4bb3KKAIsopenicillin N synthase1.21.3.10.442
4dch4DCGlucokinase2.7.1.20.442
4jx1CAMCamphor 5-monooxygenase1.14.15.10.442
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.442
1bxoPP7Penicillopepsin-13.4.23.200.441
1ot7CHCBile acid receptor/0.441
1pqc444Oxysterols receptor LXR-beta/0.441
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.441
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.441
2ok7FADFerredoxin--NADP reductase, apicoplast/0.441
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
3jzdNADMaleylacetate reductase/0.441
3k7mFAD6-hydroxy-L-nicotine oxidase/0.441
3kytHC2Nuclear receptor ROR-gamma/0.441
3toxNAPPutative oxidoreductase/0.441
3vf60H6Glucokinase2.7.1.20.441
3wmxNADNAD dependent epimerase/dehydratase/0.441
4c3yFAD3-ketosteroid dehydrogenase/0.441
4fdnFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.441
4iacACPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
4mihFADPyranose 2-oxidase1.1.3.100.441
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.441
6ctsCICCitrate synthase, mitochondrial2.3.3.10.441
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.440
1ivhCOSIsovaleryl-CoA dehydrogenase, mitochondrial1.3.8.40.440
1qorNDPQuinone oxidoreductase 1/0.440
1rf9DBRCamphor 5-monooxygenase1.14.15.10.440
2bjsACVIsopenicillin N synthase1.21.3.10.440
2dubCO8Enoyl-CoA hydratase, mitochondrial4.2.1.170.440
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.440
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
3bhrTHGThymidylate synthase/0.440
3cylVITBasic phospholipase A2 homolog piratoxin-2/0.440
3p6nDSOCamphor 5-monooxygenase1.14.15.10.440
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4bfxZVXPantothenate kinase2.7.1.330.440
4ocvANPAminoglycoside phosphotransferase/0.440