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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
3rc9TLOSugar 3-ketoreductase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3rc9TLOSugar 3-ketoreductase/1.000
3rc7TLOSugar 3-ketoreductase/0.524
2g8yNADHydroxycarboxylate dehydrogenase B/0.497
2x0eTYDWsaF/0.494
4bfxZVXPantothenate kinase2.7.1.330.494
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.493
2zc922UProthrombin3.4.21.50.491
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.486
3hxbBD5Geranylgeranyl transferase type-2 subunit beta2.5.1.600.486
1pq944BOxysterols receptor LXR-beta/0.485
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.485
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.484
3apwDP0Alpha-1-acid glycoprotein 2/0.483
1r8qAFBCytohesin-2/0.482
1r8qAFBADP-ribosylation factor 1/0.482
2zgx29UProthrombin3.4.21.50.482
1enpNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.480
2zhf49UProthrombin3.4.21.50.480
3b9lAZZSerum albumin/0.480
3h3r14HCollagen type IV alpha-3-binding protein/0.480
1upw444Oxysterols receptor LXR-beta/0.479
4f6w0SSCyclin-dependent kinase 82.7.11.220.478
3c27DKKProthrombin3.4.21.50.476
2zff53UProthrombin3.4.21.50.475
2zsbADPPantothenate kinase2.7.1.330.475
4ffmADPUncharacterized protein/0.475
2zseACPPantothenate kinase2.7.1.330.474
2tplHPPTyrosine phenol-lyase4.1.99.20.473
2zfq45UProthrombin3.4.21.50.473
4n3l2FNProthrombin3.4.21.50.473
2pksG44Prothrombin3.4.21.50.472
2zf051UProthrombin3.4.21.50.472
3f0aACOSpermidine N(1)-acetyltransferase/0.472
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.472
1d6w00RProthrombin3.4.21.50.471
1rq1FADEndoplasmic oxidoreductin-11.8.40.471
2uuk897Prothrombin3.4.21.50.471
3emlZMAAdenosine receptor A2a/0.471
1yplRA8Prothrombin3.4.21.50.470
2wwjY28Lysine-specific demethylase 4A/0.470
3eq02TSProthrombin3.4.21.50.470
4b8zGDPGDP-L-fucose synthase1.1.1.2710.470
1blzACVIsopenicillin N synthase1.21.3.10.469
1pqc444Oxysterols receptor LXR-beta/0.469
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.469
2v3hI25Prothrombin3.4.21.50.469
2zhq27UProthrombin3.4.21.50.469
4g8cC6LAlpha/beta hydrolase fold protein/0.469
1g4pFQPThiamine-phosphate synthase/0.468
2bdyUNBProthrombin3.4.21.50.468
3af0GDPPantothenate kinase2.7.1.330.468
1dggNDPCatalase1.11.1.60.467
2geuCOKPantothenate kinase2.7.1.330.467
2zhe13UProthrombin3.4.21.50.467
1f9aATPNicotinamide-nucleotide adenylyltransferase/0.466
2znk31UProthrombin3.4.21.50.466
3h3sH15Collagen type IV alpha-3-binding protein/0.466
4twnB96Ephrin type-A receptor 32.7.10.10.466
1dgfNDPCatalase1.11.1.60.465
1g9cBABBotulinum neurotoxin type B3.4.24.690.465
5kf8ACOPredicted acetyltransferase/0.465
1mueCDDProthrombin3.4.21.50.464
2bvs2CEProthrombin3.4.21.50.464
2qw8NAPEugenol synthase 11.1.1.3180.464
2zs9ADPPantothenate kinase2.7.1.330.464
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.464
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.464
3vf60H6Glucokinase2.7.1.20.464
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.464
2jh0701Prothrombin3.4.21.50.463
2zdv37UProthrombin3.4.21.50.463
2zgb21UProthrombin3.4.21.50.463
3crzFADFerredoxin--NADP+ reductase/0.463
3qpg3QPAspartate aminotransferase2.6.1.10.463
3to3ATPPetrobactin biosynthesis protein AsbB/0.463
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.463
1ry0PG2Aldo-keto reductase family 1 member C3/0.462
1yw8A75Methionine aminopeptidase 2/0.462
2v59LZKBiotin carboxylase6.3.4.140.462
3tdkUPGUDP-glucose 6-dehydrogenase1.1.1.220.462
4bb3KKAIsopenicillin N synthase1.21.3.10.462
4uyg73BBromodomain-containing protein 2/0.462
1zgv501Prothrombin3.4.21.50.461
2f3815MAldo-keto reductase family 1 member C3/0.461
5kf9ACOPredicted acetyltransferase/0.461
2rehFADNitroalkane oxidase1.7.3.10.460
2zhw12UProthrombin3.4.21.50.460
4fflADPUncharacterized protein/0.460
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.459
2xvv9DNSerum albumin/0.459
2zda32UProthrombin3.4.21.50.459
2zfr46UProthrombin3.4.21.50.459
3biu10UProthrombin3.4.21.50.459
3c16FOKAdenylate cyclase type 2/0.459
3c16FOKAdenylate cyclase type 5/0.459
3hk1B64Fatty acid-binding protein, adipocyte/0.459
3otwCOAPhosphopantetheine adenylyltransferase/0.459
3p1799PProthrombin3.4.21.50.459
4ho8THMGlucose-1-phosphate thymidylyltransferase/0.459
4omaLCSMethionine gamma-lyase/0.459
4mqt2CUMuscarinic acetylcholine receptor M2/0.459
1r5gAO1Methionine aminopeptidase 2/0.458
2bfaCB3Pteridine reductase 11.5.1.330.458
2h2aDNDProbable nicotinate-nucleotide adenylyltransferase/0.458
2r0pK2CPutative FAD-monooxygenase/0.458
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.458
3pvcFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.458
1lkdBP6Biphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.457
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.457
2hamC33Vitamin D3 receptor/0.457
4bl5GFBGDP-L-fucose synthase1.1.1.2710.457
5kgjACOPredicted acetyltransferase/0.457
1d3dBZTProthrombin3.4.21.50.456
2qx7NAPEugenol synthase 11.1.1.3180.456
2zg050UProthrombin3.4.21.50.456
3ghvGHCDihydrofolate reductase1.5.1.30.456
4ffrATPUncharacterized protein/0.456
4tjy3GNTankyrase-22.4.2.300.456
1d3pBT3Prothrombin3.4.21.50.455
1qjfACSIsopenicillin N synthase1.21.3.10.455
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
1y6qTDI5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase3.2.2.90.455
2j415GPGuanylate kinase/0.455
3pz3PZ3Geranylgeranyl transferase type-2 subunit beta2.5.1.600.455
3tfjTHGDimethylsulfonioproprionate demethylase DmdA2.1.1.2690.455
1j0b5PAPutative 1-aminocyclopropane-1-carboxylate deaminase3.5.99.70.454
1n71COAAac(6')-Ii protein/0.454
1t4v14AProthrombin3.4.21.50.454
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.454
1z71L17Prothrombin3.4.21.50.454
2gesCOKPantothenate kinase2.7.1.330.454
2jh6894Prothrombin3.4.21.50.454
3u5sFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.454
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.454
1ivrCBAAspartate aminotransferase, mitochondrial2.6.1.10.453
1re0AFBADP-ribosylation factor 1/0.453
1re0AFBARF guanine-nucleotide exchange factor 1/0.453
1s9dAFBCytohesin-2/0.453
1s9dAFBADP-ribosylation factor 1/0.453
2r2mI50Prothrombin3.4.21.50.453
3c1kT15Prothrombin3.4.21.50.453
3o15IFPThiamine-phosphate synthase/0.453
3oa2NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase/0.453
4l5b1UXDeoxycytidine kinase2.7.1.740.453
4mryCEIObelin/0.453
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.453
3p0gP0GBeta-2 adrenergic receptor/0.453
1m67BOAGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal1.1.1.80.452
1pj7FFODimethylglycine oxidase1.5.3.100.452
3nu03TUDihydrofolate reductase1.5.1.30.452
3qto10PProthrombin3.4.21.50.452
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.452
3vtdTKDVitamin D3 receptor/0.452
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.452
7catNDPCatalase1.11.1.60.452
1xjqADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.451
1xm1GAHProthrombin3.4.21.50.451
1zdwFLVPrenyltransferase/0.451
2cn0F25Prothrombin3.4.21.50.451
2r6jNDPEugenol synthase 11.1.1.3180.451
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.451
2vbpVB1Isopenicillin N synthase1.21.3.10.451
3fhxPLPPyridoxal kinase2.7.1.350.451
3mj4FADUDP-galactopyranose mutase/0.451
3ol5SAWCamphor 5-monooxygenase1.14.15.10.451
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.451
1hb1OCVIsopenicillin N synthase1.21.3.10.450
1ny2ARG_PRO_PRO_GLYProthrombin3.4.21.50.450
2ea2F77Methionine aminopeptidase 2/0.450
2vcqD25Hematopoietic prostaglandin D synthase/0.450
3mauEXTPutative sphingosine-1-phosphate lyase/0.450
3v0o4GWHisto-blood group ABO system transferase/0.450
4uugPXGBranched-chain amino acid aminotransferase, putative/0.450
5kf2COAPredicted acetyltransferase/0.450
1odnAPVIsopenicillin N synthase1.21.3.10.449
1opbRETRetinol-binding protein 2/0.449
2a9z26AAdenosine kinase2.7.1.200.449
2zfp19UProthrombin3.4.21.50.449
3c3xNAPEugenol synthase 11.1.1.3180.449
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.449
3o8gO8GHTH-type transcriptional regulator EthR/0.449
3qtv06PProthrombin3.4.21.50.449
4blcNDPCatalase1.11.1.60.449
4dpy2P0Mevalonate diphosphate decarboxylase/0.449
5cmx0G6Prothrombin3.4.21.50.449
1ascNPLAspartate aminotransferase2.6.1.10.448
1n08ADPRiboflavin kinase2.7.1.260.448
1p8dCO1Oxysterols receptor LXR-beta/0.448
1v35NAIEnoyl-ACP reductase/0.448
2acwUPGGlycosyltransferase/0.448
2nnqT4BFatty acid-binding protein, adipocyte/0.448
4e2xTYDMethyltransferase/0.448
4gdpFADPolyamine oxidase FMS1/0.448
4qa2SHHHistone deacetylase 83.5.1.980.448
4qzuRTLRetinol-binding protein 2/0.448
4v0s2HN3-dehydroquinate dehydratase4.2.1.100.448
8catNDPCatalase1.11.1.60.448
1g0rTHMGlucose-1-phosphate thymidylyltransferase/0.447
1j7uANPAminoglycoside 3'-phosphotransferase2.7.1.950.447
1nm6L86Prothrombin3.4.21.50.447
1towCRZFatty acid-binding protein, adipocyte/0.447
2piwDHTAndrogen receptor/0.447
2xpwOTCTetracycline repressor protein class D/0.447
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
3h3t16HCollagen type IV alpha-3-binding protein/0.447
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.447
3wi2P98cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4gtv7TRGeranylgeranyl transferase type-2 subunit beta2.5.1.600.447
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.446
2cf9348Prothrombin3.4.21.50.446
2fzbTOLAldose reductase1.1.1.210.446
2v58LZJBiotin carboxylase6.3.4.140.446
2wgs1AZGlutamine synthetase6.3.1.20.446
3adaNADSubunit alpha of sarocosine oxidase/0.446
3av7KYNUncharacterized protein/0.446
3fx4FX4Alcohol dehydrogenase [NADP(+)]1.1.1.20.446
3gyf51PDihydrofolate reductase1.5.1.30.446
3i2834NBifunctional epoxide hydrolase 23.3.2.100.446
3up3XCAaceDAF-12/0.446
3zkuHCVIsopenicillin N synthase1.21.3.10.446
4b68NAPL-ornithine N(5)-monooxygenase/0.446
4bamMM9Prothrombin3.4.21.50.446
4iwv1J9Glucokinase2.7.1.20.446
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.445
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.445
1lcoPPYCytochrome b2, mitochondrial1.1.2.30.445
2vqjTFGHistone deacetylase 43.5.1.980.445
3dux64UProthrombin3.4.21.50.445
3hj9FMNUncharacterized protein/0.445
3pqbVGPPutative oxidoreductase/0.445
4bqwQNMEgl nine homolog 1/0.445
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.445
4kxjP34Nucleoprotein/0.445
4msk2C8Tankyrase-12.4.2.300.445
1yrxFMNAppA protein/0.444
2ptfFMNUncharacterized protein MTH_863/0.444
2v3oI26Prothrombin3.4.21.50.444
2yx6ADPUncharacterized protein/0.444
3gyaCOAGCN5-related N-acetyltransferase/0.444
3mflDHYProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.444
3mflDHYProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.444
3p6pA6BCamphor 5-monooxygenase1.14.15.10.444
3qwc98PProthrombin3.4.21.50.444
4ax9N5NProthrombin3.4.21.50.444
4b63NAPL-ornithine N(5)-monooxygenase/0.444
4c72TLG3-oxoacyl-ACP synthase/0.444
4jlj1NMDeoxycytidine kinase2.7.1.740.444
4z87GDPInosine-5'-monophosphate dehydrogenase/0.444
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.443
1r5hAO2Methionine aminopeptidase 2/0.443
1ypeUIPProthrombin3.4.21.50.443
2pitDHTAndrogen receptor/0.443
3arvSAUChitinase A/0.443
3aw9GDUNAD-dependent epimerase/dehydratase/0.443
3zkyWT4Isopenicillin N synthase1.21.3.10.443
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
4dk70KSOxysterols receptor LXR-beta/0.443
4edz0O5Hematopoietic prostaglandin D synthase/0.443
4gaaBESLeukotriene A(4) hydrolase/0.443
1hfrMOTDihydrofolate reductase1.5.1.30.442
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
1rp4FADEndoplasmic oxidoreductin-11.8.40.442
1t4u81AProthrombin3.4.21.50.442
1zosMTM5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.442
2bktRPFRenin3.4.23.150.442
2getCOKPantothenate kinase2.7.1.330.442
2w6pOA4Biotin carboxylase6.3.4.140.442
2xf3J01Uncharacterized protein/0.442
3c1oNAPEugenol synthase/0.442
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.442
3djfBC3Purine nucleoside phosphorylase/0.442
3fr5I4AFatty acid-binding protein, adipocyte/0.442
3kslSZHProtein farnesyltransferase subunit beta2.5.1.580.442
3n61H4BNitric oxide synthase, brain1.14.13.390.442
3ns2PYVAbscisic acid receptor PYL2/0.442
3ou6SAMSAM-dependent methyltransferase/0.442
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.442
4l1fCOSAcyl-CoA dehydrogenase domain protein/0.442
4lgaA2OAbscisic acid receptor PYL2/0.442
5k2cZMAAdenosine receptor A2a/0.442
1kw9BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.441
1nceCB3Thymidylate synthase/0.441
1qiqACCIsopenicillin N synthase1.21.3.10.441
1sb1165Prothrombin3.4.21.50.441
1yw9A84Methionine aminopeptidase 2/0.441
2aclL05Oxysterols receptor LXR-alpha/0.441
2ij7TPFMycocyclosin synthase1.14.21.90.441
2iypA2P6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.441
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.441
2q3oFMN12-oxophytodienoate reductase 31.3.1.420.441
2wn6NDPADP-ribosyltransferase enzymatic component/0.441
2y6fM9FIsopenicillin N synthase1.21.3.10.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3hdqGDUUDP-galactopyranose mutase/0.441
3hu1AGSTransitional endoplasmic reticulum ATPase3.6.4.60.441
4jhiEMUNodulin-13/0.441
4jk4DIUSerum albumin/0.441
4qa0SHHHistone deacetylase 83.5.1.980.441
1dgbNDPCatalase1.11.1.60.440
1tg2H2BPhenylalanine-4-hydroxylase1.14.16.10.440
2wggTLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.440
3af3GCPPantothenate kinase2.7.1.330.440
3p67FMNPentaerythritol tetranitrate reductase/0.440
3vmmP0DAlanine--anticapsin ligase/0.440
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.440
4d6qPD2Lysine-specific demethylase 4D1.14.110.440
4eh5IRGMitogen-activated protein kinase 14/0.440
4jlm1NNDeoxycytidine kinase2.7.1.740.440
4kovKOVUncharacterized protein/0.440
4s1iPLPPyridoxal kinase, putative/0.440
4tl8AGSCircadian clock protein kinase KaiC2.7.11.10.440
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.440