sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3w2l | VRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3w2l | VRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 1.000 | |
| 3w23 | 3RO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.628 | |
| 3w1x | XRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.625 | |
| 3w2j | QRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.611 | |
| 3w1t | WRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.551 | |
| 3w1q | YRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.545 | |
| 3w2n | ROD | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.511 | |
| 3w1r | MRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.510 | |
| 3w2u | ROU | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.509 | |
| 3w3o | ROE | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.495 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.475 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.471 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.471 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.465 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.461 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.461 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.460 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.459 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.458 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.457 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.457 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.457 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.455 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.455 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 4jxr | ACO | Acetyltransferase | / | 0.452 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.452 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.451 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.451 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.450 | |
| 1b5e | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.449 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.449 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.448 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.448 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.448 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.448 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.448 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.447 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.446 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.445 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.445 | |
| 3a3g | DLZ | Lumazine protein | / | 0.445 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.445 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.444 | |
| 2jcx | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.444 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 3ty3 | GGG | Homoisocitrate dehydrogenase | 1.1.1.87 | 0.444 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.444 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.444 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.443 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.443 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.443 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.443 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.443 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.443 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.443 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.442 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.441 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.441 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.440 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.440 |