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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
4ehyADPTetraacyldisaccharide 4'-kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4ehyADPTetraacyldisaccharide 4'-kinase/1.000
3s1dZIRCytokinin dehydrogenase 11.5.99.120.499
1e2nRCAThymidine kinase/0.494
1kqcFMNOxygen-insensitive NAD(P)H nitroreductase/0.492
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.491
2z4sADPChromosomal replication initiator protein DnaA/0.484
1qiqACCIsopenicillin N synthase1.21.3.10.483
5c1mCLRMu-type opioid receptor/0.481
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.479
2r0cFADPutative FAD-monooxygenase/0.478
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.478
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
4fhf0TTSpore photoproduct lyase/0.477
2oz57XYUncharacterized protein/0.476
1kp2ATPArgininosuccinate synthase6.3.4.50.474
2a9y26AAdenosine kinase2.7.1.200.474
2rqfJH3Hemolymph juvenile hormone binding protein/0.474
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
1c7oPPGHemolysin/0.471
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
1kfbIGPTryptophan synthase alpha chain/0.469
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.469
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.469
2c29NAPDihydroflavonol 4-reductase/0.468
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.468
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
2j09FMNDeoxyribodipyrimidine photo-lyase4.1.99.30.467
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.467
2jb4A14Isopenicillin N synthase1.21.3.10.466
2rh9IGPTryptophan synthase alpha chain/0.466
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
1ay0TPPTransketolase 12.2.1.10.465
1dhfFOLDihydrofolate reductase1.5.1.30.465
1dliUDXUDP-glucose 6-dehydrogenase/0.465
2d29FADAcyl-CoA dehydrogenase/0.465
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
4dbzNDPPutative ketoacyl reductase1.3.10.465
2bu9HFVIsopenicillin N synthase1.21.3.10.464
2qimZEAClass 10 plant pathogenesis-related protein/0.463
2fj1CTCTetracycline repressor protein class D/0.461
3af3GCPPantothenate kinase2.7.1.330.461
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
4qx5CMPcGMP-dependent protein kinase 12.7.11.120.461
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.460
1obnASVIsopenicillin N synthase1.21.3.10.460
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.460
2xveFADPutative flavin-containing monooxygenase/0.460
4bfsZVSPantothenate kinase2.7.1.330.460
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.459
1rszDIHPurine nucleoside phosphorylase2.4.2.10.459
2iviACWIsopenicillin N synthase1.21.3.10.459
2v5aLZLBiotin carboxylase6.3.4.140.459
3lqfNADGalactitol dehydrogenase/0.459
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.459
1diuBDMDihydrofolate reductase1.5.1.30.458
1pd9CO4Dihydrofolate reductase1.5.1.30.458
2vprTDCTetracycline repressor protein class H/0.458
2wpxACOOrf14/0.458
3oafOAGDihydrofolate reductase1.5.1.30.458
4a862ANMajor pollen allergen Bet v 1-A/0.458
4bb3KKAIsopenicillin N synthase1.21.3.10.458
4wudANPDNA gyrase subunit B/0.458
1oc1ASVIsopenicillin N synthase1.21.3.10.457
2vkeTACTetracycline repressor protein class D/0.457
3hl0NADMaleylacetate reductase/0.457
7stdCRPScytalone dehydratase4.2.1.940.457
1qoqIGPTryptophan synthase alpha chain/0.456
2h55DZ8Heat shock protein HSP 90-alpha/0.456
2xlrFADPutative flavin-containing monooxygenase/0.456
2yj4ATPCopper-transporting ATPase/0.456
3bk2U5PRibonuclease J/0.456
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.455
2ohvNHLGlutamate racemase/0.455
3junAKDPhenazine biosynthesis protein A/B/0.455
4a83DXCMajor pollen allergen Bet v 1-A/0.455
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
4rx6ATPNitrogen regulatory PII-like protein/0.455
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.455
2z9dFMNFMN-dependent NADH-azoreductase/0.454
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.454
3to6LYS_CMCHistone acetyltransferase ESA1/0.454
4cf7ADPAdenylate kinase/0.454
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1cbqRE9Cellular retinoic acid-binding protein 2/0.453
1hb3SCVIsopenicillin N synthase1.21.3.10.453
1ia3TQ5Dihydrofolate reductase1.5.1.30.453
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.453
4auxXTCTetracycline repressor protein class D/0.453
4jl5ADPAdenylate kinase/0.453
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.453
5iw5NMNNADH pyrophosphatase/0.453
1bwsNDPGDP-L-fucose synthase/0.452
1cjtFOKAdenylate cyclase type 2/0.452
1cjtFOKAdenylate cyclase type 5/0.452
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.452
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.452
1xe65FPPlasmepsin-23.4.23.390.452
3dcsMZMCarbonic anhydrase 24.2.1.10.452
4g7gVFVLanosterol 14-alpha-demethylase/0.452
4iarERM5-hydroxytryptamine receptor 1B/0.452
1kqdFMNOxygen-insensitive NAD(P)H nitroreductase/0.451
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.451
2o7oDXTTetracycline repressor protein class D/0.451
2vbpVB1Isopenicillin N synthase1.21.3.10.451
2wi72KLHeat shock protein HSP 90-alpha/0.451
3bi6396Wee1-like protein kinase2.7.10.20.451
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3oqkS52Renin3.4.23.150.451
4cdmFO1Deoxyribodipyrimidine photolyase/0.451
4g95OAGDihydrofolate reductase1.5.1.30.451
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.451
4q73FADBifunctional protein PutA/0.451
1xddAAYIntegrin alpha-L/0.450
2j9lATPH(+)/Cl(-) exchange transporter 5/0.450
2jizANPATP synthase subunit beta, mitochondrial3.6.3.140.450
2o12FMNChorismate synthase/0.450
2oc4IMHPurine nucleoside phosphorylase2.4.2.10.450
2yphQQY2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
3zeiAWHO-acetylserine sulfhydrylase/0.450
4iijGTPTubulin alpha-1B chain/0.450
1tkaN3TTransketolase 12.2.1.10.449
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.449
2g247IGRenin3.4.23.150.449
2j83BATUlilysin3.4.240.449
3h3qH13Collagen type IV alpha-3-binding protein/0.449
3h3t16HCollagen type IV alpha-3-binding protein/0.449
3ixp834Ecdysone receptor/0.449
3kjgADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.449
3r9uFADThioredoxin reductase/0.449
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.449
4zolGTPTubulin alpha-1B chain/0.449
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.448
2zseACPPantothenate kinase2.7.1.330.448
3g5qFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.448
3pe2E1BCasein kinase II subunit alpha2.7.11.10.448
4a802ANMajor pollen allergen Bet v 1-A/0.448
4a84DXCMajor pollen allergen Bet v 1-A/0.448
4klaCHDFerrochelatase, mitochondrial4.99.1.10.448
4p9dTMPDeoxycytidylate deaminase/0.448
2g1o2IGRenin3.4.23.150.447
3f3sNADLambda-crystallin homolog/0.447
3fwgCAMCamphor 5-monooxygenase1.14.15.10.447
3gfbNADL-threonine 3-dehydrogenase/0.447
3h3r14HCollagen type IV alpha-3-binding protein/0.447
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.447
3zv64HBCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.447
4a81DXCMajor pollen allergen Bet v 1-A/0.447
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4bizADPSensor histidine kinase CpxA/0.447
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.447
1k8y13PTryptophan synthase alpha chain/0.446
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.446
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.446
3g72A6TRenin3.4.23.150.446
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.446
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.446
3p5pA3CTaxadiene synthase4.2.3.170.446
3tdaPN0Cytochrome P450 2D6/0.446
4fxy0W2Neurolysin, mitochondrial3.4.24.160.446
4opuFDAConserved Archaeal protein/0.446
4yerADPAntibiotic ABC transporter, ATP-binding protein, putative/0.446
5la6GTPTubulin alpha-1B chain/0.446
1bk0ACVIsopenicillin N synthase1.21.3.10.445
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.445
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.445
1rsgFADPolyamine oxidase FMS1/0.445
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3k4yIPEIsopentenyl phosphate kinase2.7.4.260.445
3lnc5GPGuanylate kinase/0.445
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.445
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.445
5l3dFADLysine-specific histone demethylase 1A10.445
1culFOKAdenylate cyclase type 2/0.444
1culFOKAdenylate cyclase type 5/0.444
1l8qADPChromosomal replication initiator protein DnaA/0.444
1qjfACSIsopenicillin N synthase1.21.3.10.444
1yluFMNOxygen-insensitive NAD(P)H nitroreductase/0.444
2ifaFMNUncharacterized protein/0.444
2pcaSAHDiphthine synthase/0.444
2rhgIGPTryptophan synthase alpha chain/0.444
2vkvTDCTetracycline repressor protein class D/0.444
3d9zD9ZCarbonic anhydrase 24.2.1.10.444
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.444
4l0qNADAlcohol dehydrogenase class-3/0.444
4q0kGA3Phytohormone-binding protein/0.444
4q71FADBifunctional protein PutA/0.444
4xr9NADCalS8/0.444
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.443
1mvsDTMDihydrofolate reductase1.5.1.30.443
1nghATPHeat shock cognate 71 kDa protein/0.443
1w06W05Isopenicillin N synthase1.21.3.10.443
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.443
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.443
2h15B19Carbonic anhydrase 24.2.1.10.443
2oapANPType II secretion system protein (GspE-2)/0.443
3b05FNRIsopentenyl-diphosphate delta-isomerase/0.443
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.443
4a0rDTBBifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial6.3.3.30.443
4a87NARMajor pollen allergen Bet v 1-A/0.443
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.443
4dpuAGSMevalonate diphosphate decarboxylase/0.443
4i6gFADCryptochrome-2/0.443
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.443
4wbnGTPTubulin alpha-1B chain/0.443
4zp0DXCMultidrug transporter MdfA/0.443
5irnADPNucleotide binding oligomerization domain containing 2/0.443
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.442
1osvCHCBile acid receptor/0.442
1pqc444Oxysterols receptor LXR-beta/0.442
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1wxjIPLTryptophan synthase alpha chain/0.442
2a94AP0L-lactate dehydrogenase1.1.1.270.442
2il2LIXRenin3.4.23.150.442
2p6lSAHDiphthine synthase/0.442
2vcmM11Isopenicillin N synthase1.21.3.10.442
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3mjrAC2Deoxycytidine kinase2.7.1.740.442
3ogwIMNLactoperoxidase1.11.1.70.442
4bis8HQLysine-specific demethylase 4A1.14.110.442
4mv1ADPBiotin carboxylase6.3.4.140.442
4rh10TTSpore photoproduct lyase/0.442
4s1iPLPPyridoxal kinase, putative/0.442
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
4yp12BAStimulator of interferon genes protein/0.442
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
1ppjANYCytochrome b/0.441
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.441
1xe55FEPlasmepsin-23.4.23.390.441
2g1y5IGRenin3.4.23.150.441
2iko7IGRenin3.4.23.150.441
2xpwOTCTetracycline repressor protein class D/0.441
2yoj8Y6Genome polyprotein2.7.7.480.441
3ekuCY9Actin-5C/0.441
3fr5I4AFatty acid-binding protein, adipocyte/0.441
3gqvNAPEnoyl reductase LovC10.441
3jpuTY4Transcriptional activator protein LasR/0.441
3q1kADPD-alanine--D-alanine ligase A6.3.2.40.441
3v2uATPProtein GAL3/0.441
4b3aTACTetracycline repressor protein class D/0.441
4fhd0TTSpore photoproduct lyase/0.441
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.441
4m4922YL-lactate dehydrogenase A chain1.1.1.270.441
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.441
4opgFDAConserved Archaeal protein/0.441
1knpFADL-aspartate oxidase1.4.3.160.440
1vyrFMNPentaerythritol tetranitrate reductase/0.440
1zdwFLVPrenyltransferase/0.440
2g1n1IGRenin3.4.23.150.440
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.440
2pl0STITyrosine-protein kinase Lck2.7.10.20.440
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.440
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.440
4iji99TGlutathione S-transferase-like protein YibF/0.440
4imfSI3N-acetylneuraminate lyase/0.440
4o1mNADEnoyl-acyl carrier reductase/0.440
4prxADPDNA gyrase subunit B/0.440