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
4e8wIHAD-beta-D-heptose 7-phosphate kinase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4e8wIHAD-beta-D-heptose 7-phosphate kinase/1.000
4e8yIHAD-beta-D-heptose 7-phosphate kinase/0.589
2aa0MTPAdenosine kinase2.7.1.200.518
2znq401Peroxisome proliferator-activated receptor delta/0.517
2znpK55Peroxisome proliferator-activated receptor delta/0.506
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.501
2i5bADPPyridoxine kinase/0.493
3iaeD7KBenzaldehyde lyase/0.492
2r43G3GGag-Pol polyprotein3.4.23.160.490
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.488
5c3zACPRibokinase/0.486
1gqtACPRibokinase/0.485
1xe55FEPlasmepsin-23.4.23.390.482
4a81DXCMajor pollen allergen Bet v 1-A/0.482
1npa3NHGag-Pol polyprotein3.4.23.160.480
1npwLGZGag-Pol polyprotein3.4.23.160.480
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.480
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.480
2pvyACPFibroblast growth factor receptor 2/0.477
1pjkANPCasein kinase II subunit alpha2.7.11.10.476
1ia4TQ6Dihydrofolate reductase1.5.1.30.475
3oafOAGDihydrofolate reductase1.5.1.30.475
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.474
3k4nFADPyranose 2-oxidase/0.474
3bg7FADPyranose 2-oxidase/0.473
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.473
1ia3TQ5Dihydrofolate reductase1.5.1.30.472
1rfuADPPyridoxal kinase2.7.1.350.472
2d4eNAD5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenaseiheyensis HTE831]/0.472
1d4jMSCGag-Pol polyprotein3.4.23.160.471
1k7l544Peroxisome proliferator-activated receptor alpha/0.471
3hx4ANPCalmodulin-domain protein kinase 1/0.470
3lkiATPFructokinase/0.469
2yyyNAPGlyceraldehyde-3-phosphate dehydrogenase1.2.1.590.468
4fg9ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.468
1bv9XV6Gag-Pol polyprotein3.4.23.160.467
1mrwK57Gag-Pol polyprotein3.4.23.160.467
1rrmAPRLactaldehyde reductase1.1.1.770.467
3vfa031Gag-Pol polyprotein3.4.23.160.467
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.467
4xumIMNPeroxisome proliferator-activated receptor gamma/0.467
1xddAAYIntegrin alpha-L/0.466
2z6dFMNPhototropin-22.7.11.10.466
3t1tGDPProbable gliding protein mglA/0.466
1l3iSAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)/0.465
2gn8NAPUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.465
5c3yAN2Ribokinase/0.465
1idb0DOGag-Pol polyprotein/0.464
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.464
2qnqQN3Gag-Pol polyprotein3.4.23.160.463
3hyoADPPyridoxal kinase/0.463
3vfqAR6Poly [ADP-ribose] polymerase 142.4.2.300.463
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.463
1rfvADPPyridoxal kinase2.7.1.350.462
4jin1L7RIO-type serine/threonine-protein kinase Rio12.7.11.10.462
2pdtFADVivid PAS protein VVD/0.461
2yyuC5POrotidine 5'-phosphate decarboxylase/0.461
3aidARQGag-Pol polyprotein3.4.23.160.461
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.461
4ftiH7KSerine/threonine-protein kinase Chk12.7.11.10.461
1d4hBEHGag-Pol polyprotein3.4.23.160.460
1likADNAdenosine kinase2.7.1.200.460
1sguMK1Gag-Pol polyprotein3.4.23.160.460
3h3cP1EProtein-tyrosine kinase 2-beta2.7.10.20.460
1jkx138Phosphoribosylglycinamide formyltransferase/0.459
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.459
2q5g1FAPeroxisome proliferator-activated receptor delta/0.459
2z6jTUI2-nitropropane dioxygenase/0.459
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.459
4lx9ACON-alpha-acetyltransferase2.3.10.459
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1msnJE2Gag-Pol polyprotein3.4.23.160.458
1t7kBH0Gag-Pol polyprotein3.4.23.160.458
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.458
3anxMTAPolyamine aminopropyltransferase/0.458
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.458
3gbuATPUncharacterized sugar kinase PH14592.7.10.458
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.458
4q73FADBifunctional protein PutA/0.458
1hosPHPGag-Pol polyprotein/0.457
1p31EPUUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.457
2p83MR0Beta-secretase 13.4.23.460.457
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.457
4dbzNDPPutative ketoacyl reductase1.3.10.457
4dfg0JVGag-Pol polyprotein3.4.23.160.457
4dqh017Gag-Pol polyprotein/0.457
4is3NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 21.17.98.10.457
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.457
1bdlIM1Gag-Pol polyprotein3.4.23.160.456
1bxoPP7Penicillopepsin-13.4.23.200.456
1c6yMK1Protease/0.456
1jpaANPEphrin type-B receptor 22.7.10.10.456
2a94AP0L-lactate dehydrogenase1.1.1.270.456
2fonFADAcyl-coenzyme A oxidase/0.456
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.456
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
1nvtNAPShikimate dehydrogenase (NADP(+))/0.455
1rx8NAPDihydrofolate reductase1.5.1.30.455
1w06W05Isopenicillin N synthase1.21.3.10.455
2bpv1INGag-Pol polyprotein3.4.23.160.455
2cduFADNADH oxidase/0.455
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.455
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.455
3so9017Pol protein/0.455
5a3bAPRSIR2 family protein/0.455
2xa4AZ5Tyrosine-protein kinase JAK2/0.454
3zewSTUEphrin type-B receptor 42.7.10.10.454
2cy0NAPShikimate dehydrogenase (NADP(+))/0.453
2igoFADPyranose 2-oxidase/0.453
2ylzFADPhenylacetone monooxygenase1.14.13.920.453
2ym6YM6Serine/threonine-protein kinase Chk12.7.11.10.453
3t3c017Gag-Pol polyprotein3.4.23.160.453
4ocvANPAminoglycoside phosphotransferase/0.453
5fm7ADPRuvB-like helicase/0.453
1dirNADDihydropteridine reductase1.5.1.340.452
1zp9ATPRIO-type serine/threonine-protein kinase Rio12.7.11.10.452
2w0jZATSerine/threonine-protein kinase Chk22.7.11.10.452
3h86AP5Adenylate kinase/0.452
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3keuATPPyridoxal kinase2.7.1.350.452
3lzs017Gag-Pol polyprotein3.4.23.160.452
4haiI23Bifunctional epoxide hydrolase 23.1.3.760.452
4iazADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
4mihFADPyranose 2-oxidase1.1.3.100.452
4u97STUInterleukin-1 receptor-associated kinase 42.7.11.10.452
1ahiCHO7-alpha-hydroxysteroid dehydrogenase1.1.1.1590.451
1u4dDBQActivated CDC42 kinase 1/0.451
1wbk568Pol protein/0.451
2b60RITPol polyprotein/0.451
2o65MYFSerine/threonine-protein kinase pim-12.7.11.10.451
2xrwANPMitogen-activated protein kinase 82.7.11.240.451
3a3gDLZLumazine protein/0.451
3antS82Bifunctional epoxide hydrolase 23.3.2.100.451
3bgbLJGGag-Pol polyprotein3.4.23.160.451
3pcrGTPADP-ribosylation factor 6/0.451
3rfxNADUronate dehydrogenase/0.451
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.451
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.451
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
1ec3MS3Gag-Pol polyprotein3.4.23.160.450
2i4vDJRV-1 protease/0.450
2wedPP6Penicillopepsin-13.4.23.200.450
2yxuATPPyridoxal kinase2.7.1.350.450
2zynBCDPeriplasmic binding protein/0.450
3b6zCO7Enoyl reductase LovC10.450
3oy4017Gag-Pol polyprotein3.4.23.160.450
3sa755AProtease/0.450
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.450
4gj30XPNon-receptor tyrosine-protein kinase TYK22.7.10.20.450
4gt3ATPMitogen-activated protein kinase 12.7.11.240.450
1sbgIM1Gag-Pol polyprotein/0.449
1vzdCB3Thymidylate synthase/0.449
1xe65FPPlasmepsin-23.4.23.390.449
2cgu3A3Serine/threonine-protein kinase Chk12.7.11.10.449
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.449
2r3tG4GGag-Pol polyprotein3.4.23.160.449
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.449
3ibqATPPyridoxal kinase/0.449
3qu0X40Cyclin-dependent kinase 22.7.11.220.449
4bdfH3RSerine/threonine-protein kinase Chk22.7.11.10.449
4cfdS8YIntegrase/0.449
4eji0QACytochrome P450 2A131.14.14.10.449
4fxfATPPyruvate kinase PKM2.7.1.400.449
4hjoAQ4Epidermal growth factor receptor2.7.10.10.449
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.448
1msmJE2Gag-Pol polyprotein3.4.23.160.448
1nzdUPGDNA beta-glucosyltransferase/0.448
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1xl2189Gag-Pol polyprotein3.4.23.160.448
2hxl422Serine/threonine-protein kinase Chk12.7.11.10.448
2qoqANPEphrin type-A receptor 32.7.10.10.448
2w2lNADD-mandelate dehydrogenase/0.448
3i81EBIInsulin-like growth factor 1 receptor2.7.10.10.448
3o9aK14Pol polyprotein/0.448
3qa2XNAKetohexokinase/0.448
3s1dZIRCytokinin dehydrogenase 11.5.99.120.448
4a6bQG8Gag-Pol polyprotein3.4.23.160.448
4g95OAGDihydrofolate reductase1.5.1.30.448
5byuCOAThioesterase/0.448
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.447
1h2bNAJNAD-dependent alcohol dehydrogenase/0.447
1hsgMK1Gag-Pol polyprotein/0.447
1proA88Gag-Pol polyprotein/0.447
1s3zCOAAminoglycoside N(6')-acetyltransferase type 1/0.447
1w6hTITPlasmepsin-23.4.23.390.447
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.447
2bb9AKCGag-Pol polyprotein3.4.23.160.447
2pwcG3GGag-Pol polyprotein3.4.23.160.447
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.447
3oxv478Gag-Pol polyprotein3.4.23.160.447
3pllF06Endothiapepsin3.4.23.220.447
3qf9NM8Serine/threonine-protein kinase pim-12.7.11.10.447
4euaCOASuccinyl-CoA:acetate CoA-transferase/0.447
4kip1R9Mitogen-activated protein kinase 14/0.447
5br4NADLactaldehyde reductase1.1.1.770.447
1c2tNHSPhosphoribosylglycinamide formyltransferase/0.446
1obnASVIsopenicillin N synthase1.21.3.10.446
1pnvTYDdTDP-epi-vancosaminyltransferase2.4.1.3110.446
1ppm0P1Penicillopepsin-13.4.23.200.446
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.446
2vbqBSJAminoglycoside N(6')-acetyltransferase type 1/0.446
3fl9TOPDihydrofolate reductase/0.446
3kddJZQGag-Pol polyprotein3.4.23.160.446
4a6cQG9Gag-Pol polyprotein3.4.23.160.446
4hgs15GCasein kinase I isoform gamma-32.7.11.10.446
4lj6ACPChaperone protein ClpB/0.446
4q72FADBifunctional protein PutA/0.446
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.445
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.445
2q59240Peroxisome proliferator-activated receptor gamma/0.445
2v2qNVG4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.445
3bk2U5PRibonuclease J/0.445
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3efwAK8Aurora kinase A2.7.11.10.445
3eyaTDPPyruvate dehydrogenase [ubiquinone]1.2.5.10.445
3nbvANPKetohexokinase/0.445
3tjzGNPADP-ribosylation factor 1/0.445
3uylTYDProbable NDP-rhamnosyltransferase/0.445
4kugNAD3-hydroxybutyryl-CoA dehydrogenase/0.445
4pd6URINucleoside permease/0.445
1ai9NDPDihydrofolate reductase1.5.1.30.444
1hiv1ZKGag-Pol polyprotein/0.444
1lquNDPNADPH-ferredoxin reductase FprA1.18.1.20.444
1xkdNAPIsocitrate dehydrogenase [NADP]/0.444
1yt9OISGag-Pol polyprotein/0.444
1ztfXYARIO-type serine/threonine-protein kinase Rio12.7.11.10.444
2iluNDPLactaldehyde dehydrogenase1.2.1.220.444
2ixaNADAlpha-N-acetylgalactosaminidase3.2.1.490.444
2npaMMBPeroxisome proliferator-activated receptor alpha/0.444
2ozuACOHistone acetyltransferase KAT6A/0.444
2w3bNDPDihydrofolate reductase1.5.1.30.444
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.444
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.444
3i6oGR6Gag-Pol polyprotein3.4.23.160.444
3r83Z14Cyclin-dependent kinase 22.7.11.220.444
4lhtCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.444
4orkGDPBifunctional AAC/APH2.3.10.444
4z5wILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
1bwsNDPGDP-L-fucose synthase/0.443
2hs2017Protease/0.443
2qhcAB1Protease/0.443
2r3wG3GGag-Pol polyprotein3.4.23.160.443
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.443
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.443
4bfzZVZPantothenate kinase2.7.1.330.443
4cgjNZLIntegrase/0.443
4do30LAFatty-acid amide hydrolase 13.5.1.990.443
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4i6gFADCryptochrome-2/0.443
4kwi1TJReductase homolog/0.443
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.443
4rvnCOAPhenylacetate-coenzyme A ligase/0.443
1dg8NDPDihydrofolate reductase1.5.1.30.442
1hb1OCVIsopenicillin N synthase1.21.3.10.442
1hdrNADDihydropteridine reductase1.5.1.340.442
1hiiC20Gag-Pol polyprotein/0.442
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
1qbsDMPGag-Pol polyprotein3.4.23.160.442
1qr6NADNAD-dependent malic enzyme, mitochondrial1.1.1.380.442
1w5sADPORC1-type DNA replication protein 2/0.442
2g1s4IGRenin3.4.23.150.442
2i4wKGQProtease/0.442
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.442
2wmrZYRSerine/threonine-protein kinase Chk12.7.11.10.442
3b70NAPEnoyl reductase LovC10.442
3dr8ACOL-methionine sulfoximine/L-methionine sulfone acetyltransferase/0.442
3dt1P40Mitogen-activated protein kinase 14/0.442
3el8PD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.442
3i0pNADMalate dehydrogenase, putative/0.442
3lqfNADGalactitol dehydrogenase/0.442
3nu3478Gag-Pol polyprotein3.4.23.160.442
3q71AR6Poly [ADP-ribose] polymerase 142.4.2.300.442
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.442
4ftn2HKSerine/threonine-protein kinase Chk12.7.11.10.442
4q71FADBifunctional protein PutA/0.442
5a3cNADSIR2 family protein/0.442
5j3wFMNSensory box protein/0.442
1di8DTQCyclin-dependent kinase 22.7.11.220.441
1fdoMGDFormate dehydrogenase H1.1.99.330.441
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.441
1mezGDPAdenylosuccinate synthetase isozyme 1/0.441
1tcxIM1Gag-Pol polyprotein3.4.23.160.441
2om9AJAPeroxisome proliferator-activated receptor gamma/0.441
2qd8065Gag-Pol polyprotein3.4.23.160.441
2wzgUPGUncharacterized protein/0.441
3bvb017Gag-Pol polyprotein3.4.23.160.441
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.441
3kfr3TLGag-Pol polyprotein/0.441
3sa9A68Protease/0.441
3tscNADUncharacterized protein/0.441
3wv9FEGHmd co-occurring protein HcgE/0.441
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.441
4cvlACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.441
4jbqVX6Aurora kinase A2.7.11.10.441
4n6bCOAUncharacterized protein/0.441
4wucANPDNA gyrase subunit B/0.441
5c77SAHProtein arginine N-methyltransferase SFM1/0.441
1ebyBEBGag-Pol polyprotein3.4.23.160.440
1gebCAMCamphor 5-monooxygenase1.14.15.10.440
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.440
1izhQ50Protease/0.440
1j1zATPArgininosuccinate synthase/0.440
1npvL27Gag-Pol polyprotein3.4.23.160.440
1s60COAAminoglycoside N(6')-acetyltransferase type 1/0.440
1sb8UD2WbpP/0.440
1w4xFADPhenylacetone monooxygenase1.14.13.920.440
2avsMK1Gag-Pol polyprotein3.4.23.160.440
2bpw1INGag-Pol polyprotein3.4.23.160.440
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.440
2q55MU0Protease/0.440
2qhzMZ2Gag-Pol polyprotein/0.440
2uy0HV1Gag-Pol polyprotein3.4.23.160.440
2wkz5AHGag-Pol polyprotein/0.440
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.440
3cjfSAVVascular endothelial growth factor receptor 22.7.10.10.440
3edjBCDCyclomaltodextrinase/0.440
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.440
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.440
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.440
4cesNFWIntegrase/0.440
4d03FADPhenylacetone monooxygenase1.14.13.920.440
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.440
4i02CMPcAMP-activated global transcriptional regulator CRP/0.440
4m9aFDAAcyl-CoA dehydrogenase/0.440
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
9hvp0E9Gag-Pol polyprotein/0.440