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 |
|---|---|---|---|
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 1.000 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.493 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.484 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.480 | |
| 2pnu | ENM | Androgen receptor | / | 0.475 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.471 | |
| 1osv | CHC | Bile acid receptor | / | 0.468 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.466 | |
| 1jut | LYD | Thymidylate synthase | / | 0.464 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.464 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.461 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.460 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.459 | |
| 2z6j | TUI | 2-nitropropane dioxygenase | / | 0.459 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.457 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.457 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.457 | |
| 4h3c | 0YZ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.457 | |
| 1yin | CM3 | Estrogen receptor | / | 0.456 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.456 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.455 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 4awq | 592 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.455 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.455 | |
| 1err | RAL | Estrogen receptor | / | 0.454 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.454 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.454 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.454 | |
| 4okt | 198 | Androgen receptor | / | 0.454 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.453 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 2b03 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.453 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 4lb2 | DM5 | Serum albumin | / | 0.453 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.452 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.452 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.452 | |
| 2k62 | ITL | Fatty acid-binding protein, liver | / | 0.452 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.452 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.452 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.451 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.451 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.451 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.450 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.449 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.449 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.449 | |
| 2g2f | AGS | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.448 | |
| 3reo | EUG | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.448 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.447 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.447 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.447 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.446 | |
| 2bxm | IMN | Serum albumin | / | 0.446 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.446 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.445 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.445 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.445 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.445 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.445 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.444 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.444 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.444 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.444 | |
| 2xvw | 9NR | Serum albumin | / | 0.444 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.444 | |
| 3ac2 | KSE | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.444 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.444 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.444 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.443 | |
| 1lso | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 2vf0 | F89 | Thymidylate synthase | / | 0.443 | |
| 2vmy | FFO | Serine hydroxymethyltransferase | / | 0.443 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.443 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4j4v | SVR | Nucleocapsid protein | / | 0.443 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.442 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.442 | |
| 3d7t | STU | Tyrosine-protein kinase CSK | / | 0.442 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.442 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.442 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.442 | |
| 4z9g | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.442 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.441 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2a8s | GTP | U8 snoRNA-decapping enzyme | / | 0.441 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.441 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.441 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.441 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.440 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.440 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.440 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.440 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.440 |