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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
3ibqATPPyridoxal kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3ibqATPPyridoxal kinase/1.000
1rfvADPPyridoxal kinase2.7.1.350.572
3hyoADPPyridoxal kinase/0.540
1rfuADPPyridoxal kinase2.7.1.350.526
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.509
3keuATPPyridoxal kinase2.7.1.350.500
3fhyATPPyridoxal kinase2.7.1.350.496
3hx4ANPCalmodulin-domain protein kinase 1/0.493
1bwsNDPGDP-L-fucose synthase/0.491
3u9eCOALmo1369 protein/0.489
3s1dZIRCytokinin dehydrogenase 11.5.99.120.488
2ejvNADL-threonine 3-dehydrogenase/0.487
2zbaZBATrichothecene 3-O-acetyltransferase/0.486
1nzdUPGDNA beta-glucosyltransferase/0.485
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.483
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.482
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.481
1zrzBI1Protein kinase C iota type2.7.11.130.480
2yxuATPPyridoxal kinase2.7.1.350.479
4en4ATPPyridoxal kinase2.7.1.350.479
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.476
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.476
4q71FADBifunctional protein PutA/0.476
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.476
2qo9ANPEphrin type-A receptor 32.7.10.10.475
4fv3EK6Mitogen-activated protein kinase 12.7.11.240.474
2broDF2Serine/threonine-protein kinase Chk12.7.11.10.473
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.473
1bsvNDPGDP-L-fucose synthase/0.471
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.471
2oapANPType II secretion system protein (GspE-2)/0.471
1tehNADAlcohol dehydrogenase class-31.1.1.10.470
1xddAAYIntegrin alpha-L/0.470
2vwx7X4Ephrin type-B receptor 42.7.10.10.470
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.470
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.469
4gk3L87Ephrin type-A receptor 32.7.10.10.469
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.469
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.468
3ixp834Ecdysone receptor/0.468
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.467
2qenADPWalker-Type ATPase/0.467
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.466
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.466
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.466
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.465
1kkq471Peroxisome proliferator-activated receptor alpha/0.465
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.465
3pe2E1BCasein kinase II subunit alpha2.7.11.10.465
4g2fC07Ephrin type-A receptor 32.7.10.10.465
4gk2L66Ephrin type-A receptor 32.7.10.10.465
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.465
2z1mNDPGDP-mannose 4,6-dehydratase/0.464
4tuvCPZCytochrome P450 1191.140.464
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.463
2p5uNADUDP-glucose 4-epimerase/0.463
4m83ERYOleandomycin glycosyltransferase2.4.10.463
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.462
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.462
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.462
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1xe55FEPlasmepsin-23.4.23.390.461
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.461
3tneRITCandidapepsin-13.4.23.240.461
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.461
1e3eNAIAlcohol dehydrogenase 41.1.1.10.460
1h51FMNPentaerythritol tetranitrate reductase/0.460
1zmcNADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.460
2dfvNADL-threonine 3-dehydrogenase/0.460
3nbvANPKetohexokinase/0.460
4q72FADBifunctional protein PutA/0.460
2cy0NAPShikimate dehydrogenase (NADP(+))/0.459
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.459
1g1aNADdTDP-glucose 4,6-dehydratase/0.458
4m9aFDAAcyl-CoA dehydrogenase/0.458
4rrvATP3-phosphoinositide-dependent protein kinase 12.7.11.10.458
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.457
2wxvWXVCyclin-dependent kinase 22.7.11.220.457
3qaiXNNKetohexokinase/0.457
1zemNADXylitol dehydrogenase/0.456
2xyuQ9GEphrin type-A receptor 42.7.10.10.456
4e5yNDPGDP-L-fucose synthase1.1.1.2710.456
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.456
3bbrBHYGlutamate receptor 2/0.455
3inxJZCHeat shock protein HSP 90-alpha/0.455
4b7sQLECytochrome P450 monooxygenase PikC/0.455
1h50FMNPentaerythritol tetranitrate reductase/0.454
1jmhUMPThymidylate synthase/0.454
1nvtNAPShikimate dehydrogenase (NADP(+))/0.454
1xdpATPPolyphosphate kinase/0.454
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.454
3d8vUD1Bifunctional protein GlmU/0.454
3i81EBIInsulin-like growth factor 1 receptor2.7.10.10.454
3pqbVGPPutative oxidoreductase/0.454
3umoATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.454
4bb3KKAIsopenicillin N synthase1.21.3.10.454
4bfxZVXPantothenate kinase2.7.1.330.454
4gj30XPNon-receptor tyrosine-protein kinase TYK22.7.10.20.454
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.454
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1y0s331Peroxisome proliferator-activated receptor delta/0.453
2vwz7X6Ephrin type-B receptor 42.7.10.10.453
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.453
3p8iFMNPentaerythritol tetranitrate reductase/0.453
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4fsrHKCSerine/threonine-protein kinase Chk12.7.11.10.453
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.453
4v12POGMaoC like domain protein/0.453
1sxjAGSReplication factor C subunit 1/0.452
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.452
2izrBRKCasein kinase I isoform gamma-32.7.11.10.452
2vwqNAPGlucose 1-dehydrogenase/0.452
3gbuATPUncharacterized sugar kinase PH14592.7.10.452
3wmxNADNAD dependent epimerase/dehydratase/0.452
3zs7ATPPyridoxine/pyridoxal/pyridoxamine kinase/0.452
3zuyTCHTransporter/0.452
4o0rX4ZSerine/threonine-protein kinase PAK 12.7.11.10.452
4qmxH8HSerine/threonine-protein kinase 242.7.11.10.452
4wboANWRhodopsin kinase/0.452
4xiwAZMCarbonic anhydrase, alpha type/0.452
4xumIMNPeroxisome proliferator-activated receptor gamma/0.452
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.452
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
2g226IGRenin3.4.23.150.451
2rkvZBATrichothecene 3-O-acetyltransferase/0.451
2xfsJ01Uncharacterized protein/0.451
2xj2985Serine/threonine-protein kinase pim-12.7.11.10.451
3hztJ60Calmodulin-like domain protein kinase isoform 3/0.451
3sayOFTGlycogen synthase kinase-3 beta2.7.11.260.451
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.451
4g090VDHistidinol dehydrogenase/0.451
4yaoFMNNADPH--cytochrome P450 reductase/0.451
2b7aIZATyrosine-protein kinase JAK2/0.450
2d29FADAcyl-CoA dehydrogenase/0.450
3a1nNADNDP-sugar epimerase/0.450
3c1y2BADNA integrity scanning protein DisA/0.450
3gw9VNILanosterol 14-alpha-demethylase/0.450
4a6nFADTetX family tetracycline inactivation enzyme/0.450
4a99FADTetX family tetracycline inactivation enzyme/0.450
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
5hs1VORLanosterol 14-alpha demethylase/0.450
1bygSTUTyrosine-protein kinase CSK/0.449
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.449
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.449
3b9lAZZSerum albumin/0.449
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.449
3sf6FDAGlutaryl-CoA dehydrogenase/0.449
4asuADPATP synthase subunit alpha, mitochondrial/0.449
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.449
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.449
4ly91YYGlucokinase regulatory protein/0.449
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.449
1gqtACPRibokinase/0.448
1j39UPGDNA beta-glucosyltransferase/0.448
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.448
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.448
2hk9NAPShikimate dehydrogenase (NADP(+))/0.448
2iviACWIsopenicillin N synthase1.21.3.10.448
3f03FMNPentaerythritol tetranitrate reductase/0.448
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.448
3p62FMNPentaerythritol tetranitrate reductase/0.448
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
4lj9ACPChaperone protein ClpB/0.448
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1kp3ATPArgininosuccinate synthase6.3.4.50.447
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.447
2xgoZKDUncharacterized protein/0.447
2xvdAS6Ephrin type-B receptor 42.7.10.10.447
3bhtMFRCyclin-dependent kinase 22.7.11.220.447
3etgNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.447
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.447
4c34STUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
4qmzB49Serine/threonine-protein kinase 242.7.11.10.447
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
2g5cNADPrephenate dehydrogenase/0.446
2i4qUA4Renin3.4.23.150.446
2lbaCHOFatty acid binding protein 6/0.446
2rh9IGPTryptophan synthase alpha chain/0.446
3p82FMNPentaerythritol tetranitrate reductase/0.446
3slkNDPPolyketide synthase extender module 2/0.446
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.446
4u0mGTPCyclic GMP-AMP synthase/0.446
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.446
1fxsNAPGDP-L-fucose synthase/0.445
1nooCAHCamphor 5-monooxygenase1.14.15.10.445
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.445
2fy4COACholine O-acetyltransferase2.3.1.60.445
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.445
2yn8STUEphrin type-B receptor 42.7.10.10.445
3eljGS7Mitogen-activated protein kinase 82.7.11.240.445
3tjzGNPADP-ribosylation factor 1/0.445
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.445
4e4m0NHTyrosine-protein kinase JAK2/0.445
4kkyCAMCamphor 5-monooxygenase1.14.15.10.445
4v2gITCTetracycline repressor protein class D/0.445
4wecNADShort chain dehydrogenase/0.445
4y9qC2EUncharacterized protein/0.445
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1kh3ANPArgininosuccinate synthase/0.444
1kp2ATPArgininosuccinate synthase6.3.4.50.444
1n2hPAJPantothenate synthetase6.3.2.10.444
1o9bNAIQuinate/shikimate dehydrogenase/0.444
1yw2PGJMitogen-activated protein kinase 14/0.444
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.444
2iyfERYOleandomycin glycosyltransferase2.4.10.444
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.444
2ojg19AMitogen-activated protein kinase 12.7.11.240.444
2vn0TDZCytochrome P450 2C8/0.444
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3lshFADPyranose 2-oxidase/0.444
3triNAPPyrroline-5-carboxylate reductase/0.444
4bb432WEphrin type-B receptor 42.7.10.10.444
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
5a3bAPRSIR2 family protein/0.444
1culFOKAdenylate cyclase type 2/0.443
1culFOKAdenylate cyclase type 5/0.443
1eioGCHGastrotropin/0.443
1ej2NADNicotinamide-nucleotide adenylyltransferase2.7.7.10.443
1mp0NADAlcohol dehydrogenase class-31.1.1.10.443
2uzlC94Cyclin-dependent kinase 22.7.11.220.443
2vbdV10Isopenicillin N synthase1.21.3.10.443
2vx17X8Ephrin type-B receptor 42.7.10.10.443
3cblSTUTyrosine-protein kinase Fes/Fps2.7.10.20.443
3lqfNADGalactitol dehydrogenase/0.443
3oqkS52Renin3.4.23.150.443
3q92XNBKetohexokinase/0.443
3sptUD1Bifunctional protein GlmU/0.443
4dbzNDPPutative ketoacyl reductase1.3.10.443
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.443
4ipw1G7Mycocyclosin synthase1.14.21.90.443
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.443
4yxm2BADNA integrity scanning protein DisA/0.443
1cf3FADGlucose oxidase1.1.3.40.442
1eh4IC1Casein kinase I homolog 12.7.11.10.442
1fm4DXCMajor pollen allergen Bet v 1-L/0.442
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.442
1kfbIGPTryptophan synthase alpha chain/0.442
2ev9NAPShikimate dehydrogenase (NADP(+))/0.442
2jb4A14Isopenicillin N synthase1.21.3.10.442
2vnaNAPProstaglandin reductase 21.3.1.480.442
2xx91NFGlutamate receptor 2/0.442
3a4vNADNDP-sugar epimerase/0.442
3ajrNADNDP-sugar epimerase/0.442
3cxw7CPSerine/threonine-protein kinase pim-12.7.11.10.442
3r83Z14Cyclin-dependent kinase 22.7.11.220.442
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.442
3zoiM2WIsopenicillin N synthase1.21.3.10.442
4a6cQG9Gag-Pol polyprotein3.4.23.160.442
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.442
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4gk4L90Ephrin type-A receptor 32.7.10.10.442
4uymVOR14-alpha sterol demethylase Cyp51B/0.442
1e7qNAPGDP-L-fucose synthase/0.441
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
1nhhANPDNA mismatch repair protein MutL/0.441
1ywgNADGlyceraldehyde-3-phosphate dehydrogenase/0.441
2he5NDPAldo-keto reductase family 1 member C211.1.10.441
2izuP01Casein kinase I isoform gamma-32.7.11.10.441
2po7CHDFerrochelatase, mitochondrial4.99.1.10.441
2q5g1FAPeroxisome proliferator-activated receptor delta/0.441
2wihP48Cyclin-dependent kinase 22.7.11.220.441
3atzFMNProstaglandin F2a synthase/0.441
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.441
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.441
3il1B5DGlutamate receptor 2/0.441
4e2dFMNDehydrogenase/0.441
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.441
4qmpDKISerine/threonine-protein kinase 242.7.11.10.441
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
1yi3LY2Serine/threonine-protein kinase pim-12.7.11.10.440
2dftADPShikimate kinase2.7.1.710.440
2ejzSAHDiphthine synthase/0.440
2ft9CHDFatty acid-binding protein 2, liver/0.440
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.440
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.440
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.440
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.440
2xikJ60Serine/threonine-protein kinase 252.7.11.10.440
3gwfFADCyclohexanone monooxygenase/0.440
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.440
3x2eNAIAdenosylhomocysteinase/0.440
4cukNAID-lactate dehydrogenase/0.440
4egbNADdTDP-glucose 4,6-dehydratase/0.440
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.440
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4nbwNADShort-chain dehydrogenase/reductase SDR/0.440
4q73FADBifunctional protein PutA/0.440