Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3vxj3DMDyP

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3vxj3DMDyP/1.000
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.491
2znnS44Peroxisome proliferator-activated receptor alpha/0.490
3dt1P40Mitogen-activated protein kinase 14/0.485
4jlcSU6Serine/threonine-protein kinase TBK12.7.11.10.482
3ooiSAMHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific2.1.1.430.480
4m83ERYOleandomycin glycosyltransferase2.4.10.480
3wfjNAD2-dehydropantoate 2-reductase/0.479
1bwlFMNNADPH dehydrogenase 11.6.99.10.476
1zk7FADMercuric reductase1.16.1.10.475
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.475
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.475
3i25MV7Beta-secretase 13.4.23.460.475
1jedADPSulfate adenylyltransferase/0.474
2bjfDXCCholoylglycine hydrolase3.5.1.240.474
3zuyTCHTransporter/0.474
1me6IVSPlasmepsin-23.4.23.390.473
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.473
1rx1NAPDihydrofolate reductase1.5.1.30.472
3iaeD7KBenzaldehyde lyase/0.472
3uylTYDProbable NDP-rhamnosyltransferase/0.472
4bl5GFBGDP-L-fucose synthase1.1.1.2710.472
5itzLOCTubulin beta-2B chain/0.472
2ou2ACOHistone acetyltransferase KAT5/0.471
1dhrNADDihydropteridine reductase1.5.1.340.470
1k7fIAVTryptophan synthase alpha chain/0.470
3gwfFADCyclohexanone monooxygenase/0.470
5d3qGDPDynamin-13.6.5.50.470
2ghlLIBMitogen-activated protein kinase 14/0.469
2iyfERYOleandomycin glycosyltransferase2.4.10.469
3a3gDLZLumazine protein/0.469
3drcMTXDihydrofolate reductase1.5.1.30.468
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.468
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.467
3hk1B64Fatty acid-binding protein, adipocyte/0.467
2b8v3BNBeta-secretase 13.4.23.460.465
4q73FADBifunctional protein PutA/0.465
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
1h73ANPHomoserine kinase2.7.1.390.464
3gobHXXDdmC/0.464
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.464
1a8pFADFerredoxin--NADP reductase/0.463
1di8DTQCyclin-dependent kinase 22.7.11.220.463
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.463
4b7dQLECytochrome P450 monooxygenase PikC/0.463
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4jbqVX6Aurora kinase A2.7.11.10.462
4ks7X4ZSerine/threonine-protein kinase PAK 62.7.11.10.462
1f4fTP3Thymidylate synthase/0.461
3d7kD7KBenzaldehyde lyase/0.461
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1ty9FMNPhenazine biosynthesis protein PhzG1.40.460
3fhyATPPyridoxal kinase2.7.1.350.460
3il1B5DGlutamate receptor 2/0.460
3t64DU3Deoxyuridine 5'-triphosphate nucleotidohydrolase/0.460
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.460
3v3m0ENReplicase polyprotein 1a3.4.19.120.460
4b65FADL-ornithine N(5)-monooxygenase/0.460
4ji91M3Tyrosine-protein kinase JAK2/0.460
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.460
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.459
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.458
4bb3KKAIsopenicillin N synthase1.21.3.10.458
1nzdUPGDNA beta-glucosyltransferase/0.457
2am22LGUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.457
2b3dFADModulator of drug activity B/0.457
3wmxNADNAD dependent epimerase/dehydratase/0.457
4b68FADL-ornithine N(5)-monooxygenase/0.457
1f8fNADBenzyl alcohol dehydrogenase/0.456
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
2dv4SAHDiphthine synthase/0.456
2gjlFMNNitronate monooxygenase1.13.12.160.456
2ikuLIYRenin3.4.23.150.456
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.455
3q3cNADNAD-dependent L-serine dehydrogenase/0.455
4a802ANMajor pollen allergen Bet v 1-A/0.455
4yaoFMNNADPH--cytochrome P450 reductase/0.455
4xnw2IDP2Y purinoceptor 1/0.455
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.454
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.454
1xe55FEPlasmepsin-23.4.23.390.454
2gv8NDPThiol-specific monooxygenase1.14.130.454
2qw034Z4-chlorobenzoyl CoA ligase/0.454
2r3aSAMHistone-lysine N-methyltransferase SUV39H22.1.1.430.454
2vbdV10Isopenicillin N synthase1.21.3.10.454
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.454
4mwhATPCasein kinase II subunit alpha2.7.11.10.454
4nbwNADShort-chain dehydrogenase/reductase SDR/0.454
1c2tGARPhosphoribosylglycinamide formyltransferase/0.453
1c3eGARPhosphoribosylglycinamide formyltransferase/0.453
1tqf32PBeta-secretase 13.4.23.460.453
3br3ETHTH-type transcriptional regulator QacR/0.453
3h6vNS6Glutamate receptor 2/0.453
3qlrNDPDihydrofolate reductase1.5.1.30.453
3wagTYDGlycosyltransferase/0.453
4bfsZVSPantothenate kinase2.7.1.330.453
4l4xNDPAmphI/0.453
4qecNAPElxO/0.453
4ure1PSCyclohexanol dehydrogenase/0.453
1bw9NADPhenylalanine dehydrogenase/0.452
1dj2GDPAdenylosuccinate synthetase, chloroplastic/0.452
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.452
1zrzBI1Protein kinase C iota type2.7.11.130.452
2g9uG27Glycogen phosphorylase, muscle form2.4.1.10.452
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.452
2qo9ANPEphrin type-A receptor 32.7.10.10.452
2rlcCHDCholoylglycine hydrolase3.5.1.240.452
3f7bAG5Carbonic anhydrase 44.2.1.10.452
3lxpIZANon-receptor tyrosine-protein kinase TYK22.7.10.20.452
3nmpPYVAbscisic acid receptor PYL2/0.452
3p8jFMNPentaerythritol tetranitrate reductase/0.452
3pgqGY3Acetyl-CoA carboxylase/0.452
4b63FADL-ornithine N(5)-monooxygenase/0.452
2emuSAHDiphthine synthase/0.451
3ig6438Urokinase-type plasminogen activator3.4.21.730.451
3tr05GPGuanylate kinase/0.451
4alhA9PBromodomain-containing protein 2/0.451
4ejvLCLTranscriptional regulator TcaR/0.451
4nxuADPMitochondrial dynamics protein MID51/0.451
4wx2F6FTryptophan synthase alpha chain/0.451
4wx2F6FTryptophan synthase beta chain4.2.1.200.451
1ai9NDPDihydrofolate reductase1.5.1.30.450
1ezvUQ6Cytochrome b/0.450
1kvkATPMevalonate kinase2.7.1.360.450
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.450
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.450
3imgBZ2Pantothenate synthetase6.3.2.10.450
1w0kADPATP synthase subunit alpha, mitochondrial/0.449
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.449
2gqwFADFerredoxin reductase/0.449
2x0rNADMalate dehydrogenase/0.449
3kdt7HAPeroxisome proliferator-activated receptor alpha/0.449
3wleNAD(R)-specific carbonyl reductase/0.449
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.449
4eb5PLPCysteine desulfurase IscS 2/0.449
4eqxFADCoenzyme A disulfide reductase/0.449
4fk8FADFerredoxin--NADP reductase/0.449
4fqsLYAThymidylate synthase ThyA/0.449
4ipw1G7Mycocyclosin synthase1.14.21.90.449
4jicFMNGTN Reductase/0.449
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.449
1g63FMNEpidermin decarboxylase4.1.10.448
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.448
2a1oCAMCamphor 5-monooxygenase1.14.15.10.448
2gsdNADFormate dehydrogenase/0.448
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.448
2vttLZDCyclin-dependent kinase 22.7.11.220.448
3f8rNAPNADH oxidase/thioredoxin reductase/0.448
3gxlQIGTGF-beta receptor type-12.7.11.300.448
3p62FMNPentaerythritol tetranitrate reductase/0.448
3sdkP3NProteasome subunit beta type-53.4.25.10.448
3sdkP3NProteasome subunit beta type-63.4.25.10.448
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.448
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.448
4r81FMNPredicted NADH dehydrogenase/0.448
1dr3HBIDihydrofolate reductase1.5.1.30.447
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1rb3MTXDihydrofolate reductase1.5.1.30.447
1t85CAMCamphor 5-monooxygenase1.14.15.10.447
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.447
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.447
2p8hMY9Beta-secretase 13.4.23.460.447
2q5g1FAPeroxisome proliferator-activated receptor delta/0.447
3atzFMNProstaglandin F2a synthase/0.447
3b2eADPATPase GET3/0.447
3i59N6RCRP-like cAMP-activated global transcriptional regulator/0.447
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.447
4fdpFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.447
4i1iNADMalate dehydrogenase/0.447
4ijp1EHSerine/threonine-protein kinase PRP4 homolog2.7.11.10.447
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.447
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.447
5dbgNADIridoid synthase1.3.1.990.447
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1od10QSEndothiapepsin3.4.23.220.446
1s0xC3SNuclear receptor ROR-alpha/0.446
1tj0FADBifunctional protein PutA1.5.5.20.446
1uzwCDHIsopenicillin N synthase1.21.3.10.446
1yjqNAP2-dehydropantoate 2-reductase1.1.1.1690.446
1z2nADPInositol-tetrakisphosphate 1-kinase2.7.1.1340.446
2aa3AP0L-lactate dehydrogenase/0.446
2c27ACOMycothiol acetyltransferase2.3.1.1890.446
2emrSAHDiphthine synthase/0.446
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.446
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.446
2yekEAMBromodomain-containing protein 2/0.446
3a3bRBFLumazine protein/0.446
3c1oNAPEugenol synthase/0.446
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.446
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.446
4tm1FDAKtzI/0.446
1bwsNDPGDP-L-fucose synthase/0.445
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
1g1aNADdTDP-glucose 4,6-dehydratase/0.445
1pdhFASp-hydroxybenzoate hydroxylase/0.445
1ri1GTGmRNA cap guanine-N7 methyltransferase2.1.1.560.445
1um0FMNChorismate synthase/0.445
1xddAAYIntegrin alpha-L/0.445
2dftADPShikimate kinase2.7.1.710.445
2huxSAHDiphthine synthase/0.445
2v58LZJBiotin carboxylase6.3.4.140.445
2vnhFADNADPH:ferredoxin reductase/0.445
2vwqNAPGlucose 1-dehydrogenase/0.445
2znq401Peroxisome proliferator-activated receptor delta/0.445
3a3yOBNSodium/potassium-transporting ATPase subunit alpha/0.445
3gu83GUDeath-associated protein kinase 12.7.11.10.445
3h1vTK1Glucokinase2.7.1.20.445
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.445
3o0o5ADVitamin B12-dependent ribonucleotide reductase/0.445
4a862ANMajor pollen allergen Bet v 1-A/0.445
4b1c1B1Beta-secretase 13.4.23.460.445
4hs4FMNChromate reductase/0.445
4lxhC1EAlpha/beta hydrolase fold/0.445
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.445
1lbcCYZGlutamate receptor 2/0.444
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.444
1trbFADThioredoxin reductase1.8.1.90.444
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.444
2dgnDOIAdenylosuccinate synthetase isozyme 1/0.444
2givACOHistone acetyltransferase KAT8/0.444
2hckQUETyrosine-protein kinase HCK2.7.10.20.444
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.444
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.444
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.444
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.444
3pndFADFAD:protein FMN transferase/0.444
3tjzGNPADP-ribosylation factor 1/0.444
4dc0NDPPutative ketoacyl reductase1.3.10.444
4dplNAPMalonyl-CoA reductase1.2.1.750.444
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.444
1drhNAPDihydrofolate reductase1.5.1.30.443
1jpaANPEphrin type-B receptor 22.7.10.10.443
1mczRMNBenzoylformate decarboxylase4.1.1.70.443
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
1x1cSAHC-20 methyltransferase/0.443
2b53D23Cyclin-dependent kinase 22.7.11.220.443
2qujTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.443
2xhd7T9Glutamate receptor 2/0.443
2xx91NFGlutamate receptor 2/0.443
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3ik6HCZGlutamate receptor 2/0.443
3nunJMZ3-phosphoinositide-dependent protein kinase 12.7.11.10.443
3zc5W9ZHepatocyte growth factor receptor2.7.10.10.443
4a9hTVPBromodomain-containing protein 2/0.443
4hiaFMNLOV protein/0.443
4j75TYMTryptophan--tRNA ligase/0.443
4qfxDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4v12POGMaoC like domain protein/0.443
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.443
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.443
1ez4NADL-lactate dehydrogenase1.1.1.270.442
1n3rGTPGTP cyclohydrolase 13.5.4.160.442
1thnADPAnti-sigma F factor/0.442
1x1aSAMC-20 methyltransferase/0.442
2ejzSAHDiphthine synthase/0.442
2vnjFADNADPH:ferredoxin reductase/0.442
3bbrBHYGlutamate receptor 2/0.442
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.442
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3oqkS52Renin3.4.23.150.442
3zxiTYATyrosine--tRNA ligase, mitochondrial6.1.1.10.442
3zxzKRWHepatocyte growth factor receptor2.7.10.10.442
4c3rACPAurora kinase A2.7.11.10.442
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.442
1civNAPMalate dehydrogenase [NADP], chloroplastic1.1.1.820.441
2c29NAPDihydroflavonol 4-reductase/0.441
2ftoCB3Thymidylate synthase/0.441
2g1n1IGRenin3.4.23.150.441
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.441
2pcmSAHDiphthine synthase/0.441
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.441
3isjA8DPantothenate synthetase6.3.2.10.441
3muoZPRProlyl endopeptidase/0.441
3s2v3HUGlutamate receptor ionotropic, kainate 1/0.441
3slkNDPPolyketide synthase extender module 2/0.441
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.441
4bfd8T3Beta-secretase 13.4.23.460.441
4erf0R3E3 ubiquitin-protein ligase Mdm26.3.20.441
4jxrACOAcetyltransferase/0.441
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.441
4nxxGDPMitochondrial dynamics protein MID51/0.441
4o1mNADEnoyl-acyl carrier reductase/0.441
4ylfFADDihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog/0.441
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.441
1h74ADPHomoserine kinase2.7.1.390.440
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
1qorNDPQuinone oxidoreductase 1/0.440
2a92NAIL-lactate dehydrogenase/0.440
2hxl422Serine/threonine-protein kinase Chk12.7.11.10.440
2po7CHDFerrochelatase, mitochondrial4.99.1.10.440
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.440
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.440
3a1nNADNDP-sugar epimerase/0.440
3gw9VNILanosterol 14-alpha-demethylase/0.440
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4i0j842Beta-secretase 13.4.23.460.440
4l0qNADAlcohol dehydrogenase class-3/0.440
4s1hADPPyridoxal kinase, putative/0.440
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.440
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.440
5c77SAHProtein arginine N-methyltransferase SFM1/0.440
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.440