sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2hxd | DUP | dCTP deaminase, dUMP-forming | 3.5.4.30 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2hxd | DUP | dCTP deaminase, dUMP-forming | 3.5.4.30 | 1.000 | |
| 2qxx | TTP | dCTP deaminase | 3.5.4.13 | 0.570 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.506 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.501 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.501 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.499 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.487 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.484 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.483 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.476 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.476 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.475 | |
| 4wxg | 2BO | Serine hydroxymethyltransferase | / | 0.475 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 4y0k | NAP | AntE | / | 0.473 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.472 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.472 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3glu | LYS_VAL_MET | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.471 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.469 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.468 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.465 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.465 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.464 | |
| 1fml | RTL | Retinol dehydratase | / | 0.462 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.462 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 3vet | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.460 | |
| 4u7w | NDP | MxaA | / | 0.460 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.459 | |
| 2qqf | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.458 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.458 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.457 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.454 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.454 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.454 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.454 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.454 | |
| 1g9c | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.453 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.453 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.452 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.452 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.451 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.451 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 2zsi | GA4 | Gibberellin receptor GID1A | 3 | 0.450 | |
| 3b9l | AZZ | Serum albumin | / | 0.450 | |
| 4qer | STL | Phospholipase A2 VRV-PL-VIIIa | / | 0.450 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 2gby | BRN | HTH-type transcriptional regulator QacR | / | 0.449 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.449 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.448 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.448 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.447 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.447 | |
| 3cvu | FAD | RE11660p | / | 0.446 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4b1f | KRH | Glutamate racemase | / | 0.445 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.445 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.444 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.444 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.443 | |
| 2gzl | 2AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.443 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.443 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.443 | |
| 4bz8 | J38 | Histone deacetylase | / | 0.443 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.443 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.443 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.442 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.442 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.442 | |
| 1g7u | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.441 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.441 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2j62 | GSZ | O-GlcNAcase NagJ | / | 0.440 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.440 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.440 | |
| 2wd8 | VGF | Pteridine reductase | / | 0.440 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3a20 | FMN | FMN-binding protein | / | 0.440 |