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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
5dmhADP3-oxo-tetronate kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5dmhADP3-oxo-tetronate kinase/1.000
3mddFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.499
1osvCHCBile acid receptor/0.487
1kr2TADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.481
2givACOHistone acetyltransferase KAT8/0.481
2y0mACOHistone acetyltransferase KAT8/0.475
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.472
1gqtACPRibokinase/0.471
2dteNAIGlucose 1-dehydrogenase related protein/0.470
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.470
2y05NAPProstaglandin reductase 1/0.468
3mj4FADUDP-galactopyranose mutase/0.467
2pobGW4Peroxisome proliferator-activated receptor gamma/0.465
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.464
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.462
2qu6857Vascular endothelial growth factor receptor 22.7.10.10.462
5af7FADAcyl-CoA dehydrogenase/0.462
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.461
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
1mjbACOHistone acetyltransferase ESA1/0.460
2zb3NDPProstaglandin reductase 21.3.1.480.460
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.459
4jldADPAdenylate kinase/0.459
4n6bCOAUncharacterized protein/0.459
2aa3AP0L-lactate dehydrogenase/0.458
1kevNDPNADP-dependent isopropanol dehydrogenase1.1.1.800.457
1rneC60Renin3.4.23.150.457
3gwdNAPCyclohexanone monooxygenase/0.457
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.456
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.456
3to6LYS_CMCHistone acetyltransferase ESA1/0.456
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.455
3ixj586Beta-secretase 13.4.23.460.455
3gy0NAPNAD(P)-dependent oxidoreductase/0.454
1v0jFADUDP-galactopyranose mutase5.4.99.90.453
3toxNAPPutative oxidoreductase/0.453
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.453
5jscFADPutative acyl-CoA dehydrogenase/0.453
1k7l544Peroxisome proliferator-activated receptor alpha/0.452
1kqoDNDNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.452
2he5NDPAldo-keto reductase family 1 member C211.1.10.452
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
2q8sL92Peroxisome proliferator-activated receptor gamma/0.452
3p4tFAOPutative acyl-CoA dehydrogenase/0.452
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
4q71FADBifunctional protein PutA/0.452
4qecNAPElxO/0.452
2ebaFADPutative glutaryl-CoA dehydrogenase/0.451
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.451
4dwvNAJAlcohol dehydrogenase E chain1.1.1.10.451
4jtqNAPAldo-keto reductase family 1 member C2/0.451
5fs7FADApoptosis-inducing factor 1, mitochondrial1.1.10.451
1f8fNADBenzyl alcohol dehydrogenase/0.450
1knrFADL-aspartate oxidase1.4.3.160.450
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.450
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.450
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.450
4cpdNADAlcohol dehydrogenase/0.450
4mo2FADUDP-galactopyranose mutase/0.450
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.449
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.449
2ylwFADPhenylacetone monooxygenase1.14.13.920.448
3ad9NADSubunit alpha of sarocosine oxidase/0.448
4c3yFAD3-ketosteroid dehydrogenase/0.448
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.447
3d91REMRenin3.4.23.150.447
3h86AP5Adenylate kinase/0.447
3intFDAUDP-galactopyranose mutase5.4.99.90.447
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.447
4iv6FDAIsovaleryl-CoA dehydrogenase/0.447
4nwzFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.447
4ytnFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.447
5ahsFADAcyl-CoA dehydrogenase/0.447
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.447
1ma0NADAlcohol dehydrogenase class-31.1.1.10.446
1x7dNADPutative ornithine cyclodeaminase/0.446
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.446
3b6zCO7Enoyl reductase LovC10.446
4eo3FMNBacterioferritin comigratory protein/NADH dehydrogenase/0.446
1tj0FADBifunctional protein PutA1.5.5.20.445
2c0cNAPProstaglandin reductase 310.445
2cnsACORibosomal-protein-alanine acetyltransferase/0.445
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.445
3ll9ADPIsopentenyl phosphate kinase/0.445
3nf4FADAcyl-CoA dehydrogenase domain-containing protein/0.445
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.445
4q73FADBifunctional protein PutA/0.445
3q44D50M1 family aminopeptidase3.4.110.444
5c2tFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.444
1xh6R94cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
1xhaR68cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
2cntCOARibosomal-protein-alanine acetyltransferase/0.443
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.443
3b8z294A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.443
3d3wNAPL-xylulose reductase1.1.1.100.443
4nxxGDPMitochondrial dynamics protein MID51/0.443
5ctsCMCCitrate synthase, mitochondrial2.3.3.10.443
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.443
1egdFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.442
1kkq471Peroxisome proliferator-activated receptor alpha/0.442
1mgoNADAlcohol dehydrogenase E chain1.1.1.10.442
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.442
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.442
3gw9VNILanosterol 14-alpha-demethylase/0.442
3he3FADUDP-galactopyranose mutase/0.442
3icrCOACoenzyme A disulfide reductase/0.442
1sstCOASerine acetyltransferase2.3.1.300.441
2d1cNAPIsocitrate dehydrogenase [NADP]1.1.1.420.441
3cid318Beta-secretase 13.4.23.460.441
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.441
4qi5FADCellobiose dehydrogenase/0.441
1ipeNDPTropinone reductase 21.1.1.2360.440
3gbuATPUncharacterized sugar kinase PH14592.7.10.440
4qi7FADCellobiose dehydrogenase/0.440