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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
3ingNDPHomoserine dehydrogenase related protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3ingNDPHomoserine dehydrogenase related protein/1.000
1h51FMNPentaerythritol tetranitrate reductase/0.502
1h50FMNPentaerythritol tetranitrate reductase/0.495
3p62FMNPentaerythritol tetranitrate reductase/0.494
4q71FADBifunctional protein PutA/0.489
2abbFMNPentaerythritol tetranitrate reductase/0.487
2y8qADP5'-AMP-activated protein kinase subunit gamma-1/0.487
2fznFADBifunctional protein PutA1.5.5.20.483
2is0I03Beta-secretase 13.4.23.460.483
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.483
1t2cNAIL-lactate dehydrogenase1.1.1.270.482
4jicFMNGTN Reductase/0.482
3icpNADNAD-dependent epimerase/dehydratase/0.481
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.478
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.476
3p74FMNPentaerythritol tetranitrate reductase/0.476
4blrUTPNTPase P4/0.475
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.474
2irzI02Beta-secretase 13.4.23.460.473
4q73FADBifunctional protein PutA/0.473
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.472
3f03FMNPentaerythritol tetranitrate reductase/0.472
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.472
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.471
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.471
1yqzFADCoenzyme A disulfide reductase/0.469
4df2FMNNADPH dehydrogenase/0.469
1bw9NADPhenylalanine dehydrogenase/0.468
1ma0NADAlcohol dehydrogenase class-31.1.1.10.468
3daaPDDD-alanine aminotransferase2.6.1.210.468
3o0o5ADVitamin B12-dependent ribonucleotide reductase/0.468
4e2bFMNDehydrogenase/0.468
1lf3EH5Plasmepsin-23.4.23.390.467
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.467
2ph6712Beta-secretase 13.4.23.460.467
2v9jATP5'-AMP-activated protein kinase subunit gamma-1/0.467
3orfNADDihydropteridine reductase1.5.1.340.467
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.466
1lf2R37Plasmepsin-23.4.23.390.466
1x1aSAMC-20 methyltransferase/0.466
4b79NADProbable short-chain dehydrogenase/0.466
5bt9NAP3-oxoacyl-(Acyl-carrier-protein) reductase/0.466
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.465
2xfsJ01Uncharacterized protein/0.465
3p82FMNPentaerythritol tetranitrate reductase/0.465
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.465
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.465
1x1dSAHC-20 methyltransferase/0.464
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.464
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.464
3ctyFADProbable thioredoxin reductase/0.464
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.464
3k5c0BIBeta-secretase 13.4.23.460.464
4dh60KNBeta-secretase 13.4.23.460.464
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.464
4nbwNADShort-chain dehydrogenase/reductase SDR/0.464
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
1vsoAT1Glutamate receptor ionotropic, kainate 1/0.463
1x1cSAHC-20 methyltransferase/0.463
2b8l5HABeta-secretase 13.4.23.460.463
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.463
3toxNAPPutative oxidoreductase/0.463
1f8fNADBenzyl alcohol dehydrogenase/0.462
1h63FMNPentaerythritol tetranitrate reductase/0.462
1njaDCMThymidylate synthase/0.462
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.462
3w0nANPHygromycin-B 4-O-kinase2.7.1.1630.462
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1e3sNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.461
1kr2TADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.461
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.461
3a3gDLZLumazine protein/0.461
3kb6NADD-lactate dehydrogenase/0.461
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.461
1knrFADL-aspartate oxidase1.4.3.160.460
1tj1FADBifunctional protein PutA1.5.5.20.460
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.460
2v6oFADThioredoxin glutathione reductase/0.460
3lpkZ76Beta-secretase 13.4.23.460.460
3oqfS51Renin3.4.23.150.460
4k9h1QUBeta-secretase 13.4.23.460.460
4q72FADBifunctional protein PutA/0.460
1xe55FEPlasmepsin-23.4.23.390.459
2g8yNADHydroxycarboxylate dehydrogenase B/0.459
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.459
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.459
3ko8NADNAD-dependent epimerase/dehydratase/0.459
4esoNAPPutative oxidoreductase/0.459
4frkDWDBeta-secretase 13.4.23.460.459
4h4uFADBiphenyl dioxygenase ferredoxin reductase subunit/0.459
5dp2NAPCurF/0.459
1bil0IURenin3.4.23.150.458
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.458
2a94AP0L-lactate dehydrogenase1.1.1.270.458
2hu2NADC-terminal binding protein 1/0.458
5jlaNADPutative short-chain dehydrogenase/reductase/0.458
1g1aNADdTDP-glucose 4,6-dehydratase/0.457
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.457
2zjmF1MBeta-secretase 13.4.23.460.457
3gkaFMNN-ethylmaleimide reductase/0.457
2fzwNADAlcohol dehydrogenase class-31.1.1.10.456
3clsFADElectron transfer flavoprotein subunit alpha/0.456
3lqfNADGalactitol dehydrogenase/0.456
4i02CMPcAMP-activated global transcriptional regulator CRP/0.456
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.456
4uymVOR14-alpha sterol demethylase Cyp51B/0.456
2i4uDJRProtease/0.455
2x0iNAIMalate dehydrogenase/0.455
3atzFMNProstaglandin F2a synthase/0.455
3f3sNADLambda-crystallin homolog/0.455
3iocA5DPantothenate synthetase6.3.2.10.455
3ivgFG5Pantothenate synthetase6.3.2.10.455
3p67FMNPentaerythritol tetranitrate reductase/0.455
4dieC5PCytidylate kinase/0.455
4egbNADdTDP-glucose 4,6-dehydratase/0.455
2q7vFADThioredoxin reductase/0.454
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.454
4dnaFADProbable glutathione reductase/0.454
4z875GPInosine-5'-monophosphate dehydrogenase/0.454
1h74ADPHomoserine kinase2.7.1.390.453
1kp3ATPArgininosuccinate synthase6.3.4.50.453
1kqoDNDNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.453
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.453
2vkeTACTetracycline repressor protein class D/0.453
3g2hKOTGlycogen phosphorylase, muscle form2.4.1.10.453
3lpgZ78Beta-glucuronidase3.2.1.310.453
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.453
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.453
1f52ADPGlutamine synthetase6.3.1.20.452
1geeNADGlucose 1-dehydrogenase1.1.1.470.452
1joaFADNADH peroxidase1.11.1.10.452
1ykfNAPNADP-dependent isopropanol dehydrogenase1.1.1.800.452
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.452
3gw9VNILanosterol 14-alpha-demethylase/0.452
3kpkFADSulfide-quinone reductase/0.452
4nesUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.452
4nxxGDPMitochondrial dynamics protein MID51/0.452
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.451
1ia1NDPDihydrofolate reductase1.5.1.30.451
1x1bSAHC-20 methyltransferase/0.451
2ntrL00Beta-secretase 13.4.23.460.451
2qnqQN3Gag-Pol polyprotein3.4.23.160.451
2x0rNADMalate dehydrogenase/0.451
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.451
3c1y2BADNA integrity scanning protein DisA/0.451
3dk9FADGlutathione reductase, mitochondrial1.8.1.70.451
3h2sNDPPutative NADH-flavin reductase/0.451
3k8q22APurine nucleoside phosphorylase2.4.2.10.451
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.451
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.451
4b722FBBeta-secretase 13.4.23.460.451
4cr8NADN-acylmannosamine 1-dehydrogenase1.1.1.2330.451
4f9gC2EStimulator of interferon genes protein/0.451
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.451
1i59ANPChemotaxis protein CheA2.7.13.30.450
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.450
2qtcTDKPyruvate dehydrogenase E1 component1.2.4.10.450
3qfbFADThioredoxin reductase 1, cytoplasmic1.8.1.90.450
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.450
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.450
4ips1G4Mycocyclosin synthase1.14.21.90.450
4ipw1G7Mycocyclosin synthase1.14.21.90.450
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.450
1f8wFADNADH peroxidase1.11.1.10.449
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.449
1npvL27Gag-Pol polyprotein3.4.23.160.449
1vyrFMNPentaerythritol tetranitrate reductase/0.449
2bpw1INGag-Pol polyprotein3.4.23.160.449
2p5uNADUDP-glucose 4-epimerase/0.449
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.449
3atrFDAConserved Archaeal protein/0.449
3lpfZ77Beta-glucuronidase3.2.1.310.449
3ov7ATPCCA-adding enzyme2.7.7.720.449
3ruaNADUDP-N-acetylglucosamine 4-epimerase/0.449
3sufSUEPolyprotein/0.449
3widNAPGlucose 1-dehydrogenase/0.449
4e2dFMNDehydrogenase/0.449
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.449
1c1dNAIPhenylalanine dehydrogenase/0.448
1e3eNAIAlcohol dehydrogenase 41.1.1.10.448
1xddAAYIntegrin alpha-L/0.448
1y0s331Peroxisome proliferator-activated receptor delta/0.448
2djxFMNDihydroorotate dehydrogenase (fumarate)1.3.98.10.448
2e8hSAHDiphthine synthase/0.448
2ikuLIYRenin3.4.23.150.448
3d3wNAPL-xylulose reductase1.1.1.100.448
3d84NDPDihydrofolate reductase1.5.1.30.448
3dm5GDPSignal recognition particle 54 kDa protein/0.448
4nwzFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.448
1bwlFMNNADPH dehydrogenase 11.6.99.10.447
1u4oNDDL-lactate dehydrogenase1.1.1.270.447
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.447
1wngSAHDiphthine synthase/0.447
2hsdNAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.447
3bgbLJGGag-Pol polyprotein3.4.23.160.447
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.447
3oqkS52Renin3.4.23.150.447
3raiX85Cyclin-dependent kinase 22.7.11.220.447
3zh8C58Protein kinase C iota type2.7.11.130.447
4ambDUDPutative glycosyl transferase/0.447
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.447
4fryNADPutative signal-transduction protein with CBS domains/0.447
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.447
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.447
5choFADFlavin reductase/0.447
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.446
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.446
2iyfERYOleandomycin glycosyltransferase2.4.10.446
2nvkFADThioredoxin reductase 1, mitochondrial1.8.1.90.446
2oorNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.446
2vkmBSDBeta-secretase 13.4.23.460.446
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.446
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.446
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.446
4j2wFADKynurenine 3-monooxygenase/0.446
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
2aa3AP0L-lactate dehydrogenase/0.445
2dsgSAHDiphthine synthase/0.445
2e4nSAHDiphthine synthase/0.445
2g226IGRenin3.4.23.150.445
2g247IGRenin3.4.23.150.445
2j3nFADThioredoxin reductase 1, cytoplasmic1.8.1.90.445
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.445
3pm9FADPutative oxidoreductase/0.445
3qlsNDPDihydrofolate reductase1.5.1.30.445
3tjlFMNNADPH dehydrogenase/0.445
4ejmNAPPutative zinc-binding dehydrogenase/0.445
4j31FADKynurenine 3-monooxygenase/0.445
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.445
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.444
1g6kNADGlucose 1-dehydrogenase1.1.1.470.444
1jmgUMPThymidylate synthase/0.444
1kp2ATPArgininosuccinate synthase6.3.4.50.444
1rwbNADGlucose 1-dehydrogenase1.1.1.470.444
1t7kBH0Gag-Pol polyprotein3.4.23.160.444
2gv8NDPThiol-specific monooxygenase1.14.130.444
2iko7IGRenin3.4.23.150.444
2v5aLZLBiotin carboxylase6.3.4.140.444
2vprTDCTetracycline repressor protein class H/0.444
2xpwOTCTetracycline repressor protein class D/0.444
3bgcLJHGag-Pol polyprotein3.4.23.160.444
3ig6438Urokinase-type plasminogen activator3.4.21.730.444
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.444
3w8eNAD3-hydroxybutyrate dehydrogenase/0.444
4opgFDAConserved Archaeal protein/0.444
4y95746Tyrosine-protein kinase/0.444
4yagNAIC alpha-dehydrogenase/0.444
5c2tFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.444
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.444
5i4nATPTyrosine-protein kinase JAK2/0.444
5irnADPNucleotide binding oligomerization domain containing 2/0.444
1gcoNADGlucose 1-dehydrogenase1.1.1.470.443
1j1zATPArgininosuccinate synthase/0.443
1omoNADAlanine dehydrogenase/0.443
1vzbUMPThymidylate synthase/0.443
1zrqFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.443
2f3rG5PGuanylate kinase2.7.4.80.443
2gh5FADGlutathione reductase, mitochondrial1.8.1.70.443
2givACOHistone acetyltransferase KAT8/0.443
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.443
2p6lSAHDiphthine synthase/0.443
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.443
3ms421NGlycogen phosphorylase, muscle form2.4.1.10.443
3o0qADNVitamin B12-dependent ribonucleotide reductase/0.443
3o3pGDDGlycosyl transferase, family 2/0.443
3o96IQORAC-alpha serine/threonine-protein kinase2.7.11.10.443
3o9hK2EGag-Pol polyprotein/0.443
4lk3NADUDP-glucuronic acid decarboxylase 14.1.1.350.443
4xd1T3QQdtf/0.443
1dr2TAPDihydrofolate reductase1.5.1.30.442
1gqtACPRibokinase/0.442
1i6kTYMTryptophan--tRNA ligase6.1.1.20.442
1j4jACOAcetyltransferase2.3.10.442
1k7fIAVTryptophan synthase alpha chain/0.442
1msmJE2Gag-Pol polyprotein3.4.23.160.442
2ek2SAHDiphthine synthase/0.442
2g1n1IGRenin3.4.23.150.442
2geuCOKPantothenate kinase2.7.1.330.442
2gjlFMNNitronate monooxygenase1.13.12.160.442
2ifaFMNUncharacterized protein/0.442
2il2LIXRenin3.4.23.150.442
2ixaNADAlpha-N-acetylgalactosaminidase3.2.1.490.442
2x9dITCTetracycline repressor protein class D/0.442
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.442
3djjFADGlutathione reductase, mitochondrial1.8.1.70.442
3ed1GA3Gibberellin receptor GID1/0.442
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.442
3nbvANPKetohexokinase/0.442
4dpf0LGBeta-secretase 13.4.23.460.442
4k6fNAPPutative Acetoacetyl-CoA reductase/0.442
4m55NADUDP-glucuronic acid decarboxylase 14.1.1.350.442
4qaiFMNNADPH dehydrogenase/0.442
4qecNAPElxO/0.442
5d3qGDPDynamin-13.6.5.50.442
1cf3FADGlucose oxidase1.1.3.40.441
1d0mBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.441
1dirNADDihydropteridine reductase1.5.1.340.441
1k6cMK1Gag-Pol polyprotein3.4.23.160.441
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1l7x700Glycogen phosphorylase, liver form2.4.1.10.441
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.441
1p5rCOAFormyl-CoA:oxalate CoA-transferase/0.441
1tj2FADBifunctional protein PutA1.5.5.20.441
1w0kADPATP synthase subunit alpha, mitochondrial/0.441
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.441
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.441
2omeNADC-terminal-binding protein 2/0.441
2w06FRVCyclin-dependent kinase 22.7.11.220.441
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.441
3atyFMNProstaglandin F2a synthase/0.441
3i12ADPD-alanine--D-alanine ligase A6.3.2.40.441
3ixj586Beta-secretase 13.4.23.460.441
3qwbNDPProbable quinone oxidoreductase1.6.5.50.441
3zhsTD6Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.441
4bvbAR6NAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.441
4h6kFMNNADPH dehydrogenase 11.6.99.10.441
4px9ADPATP-dependent RNA helicase DDX3X3.6.4.130.441
1ae1NAPTropinone reductase 1/0.440
1tehNADAlcohol dehydrogenase class-31.1.1.10.440
1tj0FADBifunctional protein PutA1.5.5.20.440
1w6hTITPlasmepsin-23.4.23.390.440
2ignFADPyranose 2-oxidase/0.440
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.440
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.440
3h3jNADL-lactate dehydrogenase 11.1.1.270.440
3mk6ACOPantothenate kinase 32.7.1.330.440
3sf6FDAGlutaryl-CoA dehydrogenase/0.440
3vg10GTBeta-secretase 13.4.23.460.440
3vydVYDRenin3.4.23.150.440
4aa4QC0Mitogen-activated protein kinase 14/0.440
4cukNAID-lactate dehydrogenase/0.440
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.440
4rvgTYDD-mycarose 3-C-methyltransferase/0.440
4xczFONQdtf/0.440
4yaoFMNNADPH--cytochrome P450 reductase/0.440
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.440