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 |
|---|---|---|---|
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 1.000 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.470 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.470 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.469 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.464 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.463 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.463 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.460 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.459 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.459 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.458 | |
| 3bnk | FMN | Flavoredoxin | / | 0.455 | |
| 4xr9 | NAD | CalS8 | / | 0.455 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.454 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.454 | |
| 5cho | FAD | Flavin reductase | / | 0.454 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.453 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.452 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.452 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.451 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.451 | |
| 3v2u | ATP | Protein GAL3 | / | 0.451 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.450 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.449 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.448 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.448 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.447 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.447 | |
| 4fdu | IHS | Putative multiple inositol polyphosphate histidine phosphatase 1 | / | 0.447 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.446 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.446 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.446 | |
| 4bjz | FAD | Probable salicylate monooxygenase | / | 0.446 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.446 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.445 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.444 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.444 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.444 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.442 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.442 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.441 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.441 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.441 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.441 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.440 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.440 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.440 |