Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3ibqATPPyridoxal kinase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3ibqATPPyridoxal kinase/1.000
1rfvADPPyridoxal kinase2.7.1.350.554
3hyoADPPyridoxal kinase/0.528
1rfuADPPyridoxal kinase2.7.1.350.524
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.509
1nzdUPGDNA beta-glucosyltransferase/0.491
3hx4ANPCalmodulin-domain protein kinase 1/0.491
3s1dZIRCytokinin dehydrogenase 11.5.99.120.490
4gncASORegucalcin3.1.1.170.487
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.486
2zbaZBATrichothecene 3-O-acetyltransferase/0.486
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.486
3u9eCOALmo1369 protein/0.485
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.481
3lqfNADGalactitol dehydrogenase/0.481
4q71FADBifunctional protein PutA/0.481
1zrzBI1Protein kinase C iota type2.7.11.130.480
1dz8CAMCamphor 5-monooxygenase1.14.15.10.479
3keuATPPyridoxal kinase2.7.1.350.477
3p62FMNPentaerythritol tetranitrate reductase/0.477
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.477
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.476
4l4eCAMCamphor 5-monooxygenase1.14.15.10.476
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.475
2qo9ANPEphrin type-A receptor 32.7.10.10.474
1h51FMNPentaerythritol tetranitrate reductase/0.473
3ixp834Ecdysone receptor/0.473
1xe55FEPlasmepsin-23.4.23.390.472
2broDF2Serine/threonine-protein kinase Chk12.7.11.10.472
3fhyATPPyridoxal kinase2.7.1.350.472
3fwjCAMCamphor 5-monooxygenase1.14.15.10.472
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.471
2yxuATPPyridoxal kinase2.7.1.350.471
4fv3EK6Mitogen-activated protein kinase 12.7.11.240.471
2vwx7X4Ephrin type-B receptor 42.7.10.10.470
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.470
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.469
4gk3L87Ephrin type-A receptor 32.7.10.10.469
4k28NADShikimate dehydrogenase family protein/0.469
1h50FMNPentaerythritol tetranitrate reductase/0.468
1ykdCMPAdenylate cyclase/0.467
2ejvNADL-threonine 3-dehydrogenase/0.467
1t87CAMCamphor 5-monooxygenase1.14.15.10.466
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.466
1xddAAYIntegrin alpha-L/0.466
2qenADPWalker-Type ATPase/0.466
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.465
4b99R4LMitogen-activated protein kinase 72.7.11.240.465
4g2fC07Ephrin type-A receptor 32.7.10.10.465
4gk2L66Ephrin type-A receptor 32.7.10.10.465
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.464
1j39UPGDNA beta-glucosyltransferase/0.464
1kkq471Peroxisome proliferator-activated receptor alpha/0.464
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.464
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.464
4dbzNDPPutative ketoacyl reductase1.3.10.464
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.464
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
2dfvNADL-threonine 3-dehydrogenase/0.463
1bwsNDPGDP-L-fucose synthase/0.462
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.462
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.462
4l4fCAMCamphor 5-monooxygenase1.14.15.10.462
1t86CAMCamphor 5-monooxygenase1.14.15.10.461
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.461
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.461
3uk6ADPRuvB-like 23.6.4.120.461
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.460
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
2ath3EAPeroxisome proliferator-activated receptor gamma/0.460
2p5uNADUDP-glucose 4-epimerase/0.460
3bbrBHYGlutamate receptor 2/0.460
3p8iFMNPentaerythritol tetranitrate reductase/0.460
3qt62P0Mevalonate diphosphate decarboxylase/0.460
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
4q72FADBifunctional protein PutA/0.460
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1a72PADAlcohol dehydrogenase E chain1.1.1.10.459
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.459
1o76CAMCamphor 5-monooxygenase1.14.15.10.459
2fy4COACholine O-acetyltransferase2.3.1.60.459
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.459
2oapANPType II secretion system protein (GspE-2)/0.459
2oo5TXDNAD(P) transhydrogenase subunit alpha part 11.6.1.20.459
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.459
3qaiXNNKetohexokinase/0.459
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.458
2a1nCAMCamphor 5-monooxygenase1.14.15.10.458
2cy0NAPShikimate dehydrogenase (NADP(+))/0.458
2vxoXMPGMP synthase [glutamine-hydrolyzing]6.3.5.20.458
3triNAPPyrroline-5-carboxylate reductase/0.458
4rrvATP3-phosphoinositide-dependent protein kinase 12.7.11.10.458
1bk0ACVIsopenicillin N synthase1.21.3.10.457
3pe2E1BCasein kinase II subunit alpha2.7.11.10.457
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.457
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.457
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.457
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.457
1bsvNDPGDP-L-fucose synthase/0.456
1kfbIGPTryptophan synthase alpha chain/0.456
1omoNADAlanine dehydrogenase/0.456
1tehNADAlcohol dehydrogenase class-31.1.1.10.456
1uyuCAMCamphor 5-monooxygenase1.14.15.10.456
1zemNADXylitol dehydrogenase/0.456
2wxvWXVCyclin-dependent kinase 22.7.11.220.456
2xyuQ9GEphrin type-A receptor 42.7.10.10.456
3cjfSAVVascular endothelial growth factor receptor 22.7.10.10.456
3p74FMNPentaerythritol tetranitrate reductase/0.456
3vyfVYFRenin3.4.23.150.456
3wrmCAMCamphor 5-monooxygenase1.14.15.10.456
4ek1CAMCamphor 5-monooxygenase1.14.15.10.456
4fsrHKCSerine/threonine-protein kinase Chk12.7.11.10.456
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.455
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.455
1g1aNADdTDP-glucose 4,6-dehydratase/0.455
1x2hLPALipoate-protein ligase A6.3.1.200.455
2a1mCAMCamphor 5-monooxygenase1.14.15.10.455
2a1oCAMCamphor 5-monooxygenase1.14.15.10.455
3d4pNADL-lactate dehydrogenase 11.1.1.270.455
3fwgCAMCamphor 5-monooxygenase1.14.15.10.455
3wrhCAMCamphor 5-monooxygenase1.14.15.10.455
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.455
4h4qFADBiphenyl dioxygenase ferredoxin reductase subunit/0.455
4m83ERYOleandomycin glycosyltransferase2.4.10.455
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.455
6cp4CAMCamphor 5-monooxygenase1.14.15.10.455
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1jmhUMPThymidylate synthase/0.454
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.454
3fwfCAMCamphor 5-monooxygenase1.14.15.10.454
3i81EBIInsulin-like growth factor 1 receptor2.7.10.10.454
3p82FMNPentaerythritol tetranitrate reductase/0.454
3pe6ZYHMonoglyceride lipase/0.454
3wmxNADNAD dependent epimerase/dehydratase/0.454
4gj30XPNon-receptor tyrosine-protein kinase TYK22.7.10.20.454
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.454
1xdpATPPolyphosphate kinase/0.453
2b7aIZATyrosine-protein kinase JAK2/0.453
2vwz7X6Ephrin type-B receptor 42.7.10.10.453
2zaxCAMCamphor 5-monooxygenase1.14.15.10.453
3junAKDPhenazine biosynthesis protein A/B/0.453
1e3eNAIAlcohol dehydrogenase 41.1.1.10.452
2izrBRKCasein kinase I isoform gamma-32.7.11.10.452
3bhtMFRCyclin-dependent kinase 22.7.11.220.452
3zs7ATPPyridoxine/pyridoxal/pyridoxamine kinase/0.452
4en4ATPPyridoxal kinase2.7.1.350.452
4qmxH8HSerine/threonine-protein kinase 242.7.11.10.452
5cyoGDPSeptin-9/0.452
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
2rkvZBATrichothecene 3-O-acetyltransferase/0.451
2vwqNAPGlucose 1-dehydrogenase/0.451
2xj2985Serine/threonine-protein kinase pim-12.7.11.10.451
2xvdAS6Ephrin type-B receptor 42.7.10.10.451
3gwfFADCyclohexanone monooxygenase/0.451
3hztJ60Calmodulin-like domain protein kinase isoform 3/0.451
3l63CAMCamphor 5-monooxygenase1.14.15.10.451
4a8v2ANMajor pollen allergen Bet v 1-J/0.451
4a99FADTetX family tetracycline inactivation enzyme/0.451
4qmzB49Serine/threonine-protein kinase 242.7.11.10.451
1dz4CAMCamphor 5-monooxygenase1.14.15.10.450
1sxjAGSReplication factor C subunit 1/0.450
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.450
2znq401Peroxisome proliferator-activated receptor delta/0.450
3gbuATPUncharacterized sugar kinase PH14592.7.10.450
3inxJZCHeat shock protein HSP 90-alpha/0.450
4m9aFDAAcyl-CoA dehydrogenase/0.450
5bsgNAPPyrroline-5-carboxylate reductase/0.450
5eccNAPDehydrofolate reductase type I/0.450
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
2feuCAMCamphor 5-monooxygenase1.14.15.10.449
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.449
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
3lshFADPyranose 2-oxidase/0.449
3tz3B36Acetyl-CoA carboxylase/0.449
3vthAPCCarbamoyltransferase/0.449
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.449
4l4cCAMCamphor 5-monooxygenase1.14.15.10.449
4yx6FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.449
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.448
1kp2ATPArgininosuccinate synthase6.3.4.50.448
1nvtNAPShikimate dehydrogenase (NADP(+))/0.448
1qr6NADNAD-dependent malic enzyme, mitochondrial1.1.1.380.448
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.448
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.448
3tneRITCandidapepsin-13.4.23.240.448
4g7gVFVLanosterol 14-alpha-demethylase/0.448
4ly91YYGlucokinase regulatory protein/0.448
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.448
5fwnNAPPutative dehydrogenase/0.448
1d2sDHTSex hormone-binding globulin/0.447
2qbnCAMCamphor 5-monooxygenase1.14.15.10.447
3a1nNADNDP-sugar epimerase/0.447
3qlrNDPDihydrofolate reductase1.5.1.30.447
3vydVYDRenin3.4.23.150.447
3wrlCAMCamphor 5-monooxygenase1.14.15.10.447
3zuyTCHTransporter/0.447
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
4du82P0Mevalonate diphosphate decarboxylase/0.447
4g090VDHistidinol dehydrogenase/0.447
4lj9ACPChaperone protein ClpB/0.447
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.446
1q5kTMUGlycogen synthase kinase-3 beta2.7.11.260.446
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.446
3nbvANPKetohexokinase/0.446
4bfxZVXPantothenate kinase2.7.1.330.446
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.446
4mf029ZTyrosine-protein kinase ITK/TSK2.7.10.20.446
4qmpDKISerine/threonine-protein kinase 242.7.11.10.446
4xumIMNPeroxisome proliferator-activated receptor gamma/0.446
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.445
1t88CAMCamphor 5-monooxygenase1.14.15.10.445
2abbFMNPentaerythritol tetranitrate reductase/0.445
2xgoZKDUncharacterized protein/0.445
2ydiYDISerine/threonine-protein kinase Chk12.7.11.10.445
2yn8STUEphrin type-B receptor 42.7.10.10.445
3eljGS7Mitogen-activated protein kinase 82.7.11.240.445
3q1kADPD-alanine--D-alanine ligase A6.3.2.40.445
3w3oROEDihydroorotate dehydrogenase (fumarate)1.3.98.10.445
4kl9NDPDihydrofolate reductase1.5.1.30.445
4u0mGTPCyclic GMP-AMP synthase/0.445
4y9qC2EUncharacterized protein/0.445
5a3bAPRSIR2 family protein/0.445
1dz6CAMCamphor 5-monooxygenase1.14.15.10.444
1nhhANPDNA mismatch repair protein MutL/0.444
1yrcCAMCamphor 5-monooxygenase1.14.15.10.444
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.444
2he5NDPAldo-keto reductase family 1 member C211.1.10.444
2q9fC3SCholesterol 24-hydroxylase/0.444
2qblCAMCamphor 5-monooxygenase1.14.15.10.444
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
3a4vNADNDP-sugar epimerase/0.444
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.444
3drcMTXDihydrofolate reductase1.5.1.30.444
3l9hEMQKinesin-like protein KIF11/0.444
4a6nFADTetX family tetracycline inactivation enzyme/0.444
4cr8NADN-acylmannosamine 1-dehydrogenase1.1.1.2330.444
4ddhMS0Pantothenate synthetase6.3.2.10.444
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1ay0TPPTransketolase 12.2.1.10.443
1ej2NADNicotinamide-nucleotide adenylyltransferase2.7.7.10.443
1kh3ANPArgininosuccinate synthase/0.443
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.443
1nooCAHCamphor 5-monooxygenase1.14.15.10.443
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
1yrdCAMCamphor 5-monooxygenase1.14.15.10.443
1yw2PGJMitogen-activated protein kinase 14/0.443
2gqwFADFerredoxin reductase/0.443
2iviACWIsopenicillin N synthase1.21.3.10.443
2iyfERYOleandomycin glycosyltransferase2.4.10.443
2ojg19AMitogen-activated protein kinase 12.7.11.240.443
2uzlC94Cyclin-dependent kinase 22.7.11.220.443
2vx17X8Ephrin type-B receptor 42.7.10.10.443
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.443
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
3atzFMNProstaglandin F2a synthase/0.443
3b9lAZZSerum albumin/0.443
3d8vUD1Bifunctional protein GlmU/0.443
3imgBZ3Pantothenate synthetase6.3.2.10.443
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.443
3r9uFADThioredoxin reductase/0.443
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.443
3tvuB37Acetyl-CoA carboxylase/0.443
4asuADPATP synthase subunit alpha, mitochondrial/0.443
4bb432WEphrin type-B receptor 42.7.10.10.443
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.443
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.443
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4wboANWRhodopsin kinase/0.443
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
2y6o1N1Ephrin type-A receptor 42.7.10.10.442
3cxw7CPSerine/threonine-protein kinase pim-12.7.11.10.442
3eldSFGMethyltransferase/0.442
3pqbVGPPutative oxidoreductase/0.442
3sf6FDAGlutaryl-CoA dehydrogenase/0.442
4a6cQG9Gag-Pol polyprotein3.4.23.160.442
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.442
4v2gITCTetracycline repressor protein class D/0.442
1a59COA2-methylcitrate synthase/0.441
1e1kFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.441
1y0s331Peroxisome proliferator-activated receptor delta/0.441
2qbmCAMCamphor 5-monooxygenase1.14.15.10.441
2xikJ60Serine/threonine-protein kinase 252.7.11.10.441
3etgNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.441
3f03FMNPentaerythritol tetranitrate reductase/0.441
3fwiCAMCamphor 5-monooxygenase1.14.15.10.441
3ictFADCoenzyme A disulfide reductase/0.441
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.441
3slkNDPPolyketide synthase extender module 2/0.441
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.441
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.441
4hy6FJ1Heat shock protein HSP 90-alpha/0.441
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.441
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
1eh4IC1Casein kinase I homolog 12.7.11.10.440
1fmjRTLRetinol dehydratase/0.440
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.440
1nzfUPGDNA beta-glucosyltransferase/0.440
1yi3LY2Serine/threonine-protein kinase pim-12.7.11.10.440
2d29FADAcyl-CoA dehydrogenase/0.440
2izuP01Casein kinase I isoform gamma-32.7.11.10.440
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.440
2wihP48Cyclin-dependent kinase 22.7.11.220.440
2wmqZYQSerine/threonine-protein kinase Chk12.7.11.10.440
3ajrNADNDP-sugar epimerase/0.440
3mjhGTPRas-related protein Rab-5A/0.440
3phiNDPShikimate dehydrogenase (NADP(+))/0.440
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.440
3tnlNADShikimate dehydrogenase (NADP(+))/0.440
4nbwNADShort-chain dehydrogenase/reductase SDR/0.440
4q73FADBifunctional protein PutA/0.440
4tuvCPZCytochrome P450 1191.140.440
4u7wNDPMxaA/0.440
4yqfGDPSeptin-9/0.440