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 |
|---|---|---|---|
| 1r6a | SAH | Genome polyprotein | 2.7.7.48 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1r6a | SAH | Genome polyprotein | 2.7.7.48 | 1.000 | |
| 2p1d | SAH | Genome polyprotein | 2.7.7.48 | 0.655 | |
| 1l9k | SAH | Genome polyprotein | 2.7.7.48 | 0.609 | |
| 2p3q | SAH | Genome polyprotein | / | 0.598 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.581 | |
| 4ctj | SAM | Genome polyprotein | / | 0.546 | |
| 3eld | SFG | Methyltransferase | / | 0.536 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.532 | |
| 3elu | SAM | Methyltransferase | / | 0.532 | |
| 2oxt | SAM | Genome polyprotein | / | 0.529 | |
| 3evc | SAH | Genome polyprotein | 2.1.1.56 | 0.525 | |
| 3p97 | SAM | Genome polyprotein | 2.1.1.56 | 0.521 | |
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 0.513 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.507 | |
| 5jjr | SAH | Genome polyprotein | / | 0.504 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.491 | |
| 3ely | SAH | Methyltransferase | / | 0.490 | |
| 5cuq | NSC | Genome polyprotein | / | 0.490 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.488 | |
| 5jjs | SAH | Genome polyprotein | / | 0.483 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.480 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.471 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.470 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.469 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.467 | |
| 1pl8 | NAD | Sorbitol dehydrogenase | 1.1.1.14 | 0.466 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.464 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.462 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.461 | |
| 1kzi | THG | Thymidylate synthase | / | 0.459 | |
| 5dto | SAH | Genome polyprotein | / | 0.459 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.457 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.457 | |
| 2bxq | IMN | Serum albumin | / | 0.456 | |
| 3thr | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.456 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.455 | |
| 3eej | 53R | Uncharacterized protein | / | 0.455 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.453 | |
| 4l8u | 9AZ | Serum albumin | / | 0.453 | |
| 1yqj | 6NP | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.452 | |
| 2x1n | X1N | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.451 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3eem | 53V | Uncharacterized protein | / | 0.449 | |
| 3ez2 | ADP | Plasmid partition protein A | / | 0.449 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.448 | |
| 2yx6 | ADP | Uncharacterized protein | / | 0.448 | |
| 3b9l | AZZ | Serum albumin | / | 0.448 | |
| 1jm6 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.447 | |
| 2hk5 | 1BM | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.447 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.446 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.446 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 3cgd | COA | Coenzyme A disulfide reductase | / | 0.446 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.446 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.445 | |
| 2itn | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2xvv | 9DN | Serum albumin | / | 0.445 | |
| 4mf0 | 29Z | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.445 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.444 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.444 | |
| 2kce | D16 | Thymidylate synthase | / | 0.444 | |
| 3qly | 55V | Uncharacterized protein | / | 0.444 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.444 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.443 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.443 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.443 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.443 | |
| 1f28 | UMP | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.442 | |
| 1m17 | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 2itt | AEE | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.442 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.442 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.442 | |
| 4a31 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4equ | G6I | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.442 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.441 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.441 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.441 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.441 | |
| 5c03 | AGS | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.441 | |
| 1axw | MTX | Thymidylate synthase | / | 0.440 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 2acw | UPG | Glycosyltransferase | / | 0.440 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.440 | |
| 2w6n | OA2 | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 3exn | ACO | Probable acetyltransferase | / | 0.440 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3fr8 | NDP | Ketol-acid reductoisomerase, chloroplastic | 1.1.1.86 | 0.440 | |
| 4ft3 | H1K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 |