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 |
|---|---|---|---|
| 4kxn | 6K6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4kxn | 6K6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 1.000 | |
| 4kxl | 6C6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.568 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.509 | |
| 1oiy | N41 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.490 | |
| 3r34 | COA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.484 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.483 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.481 | |
| 4ap1 | FAD | Steroid monooxygenase | / | 0.474 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.471 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.468 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.468 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.468 | |
| 4l4x | NDP | AmphI | / | 0.468 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.466 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.466 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.465 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.464 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.463 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.463 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.463 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.463 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.462 | |
| 2xk9 | XK9 | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.462 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.462 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.461 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.461 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.461 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.460 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.460 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.459 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.458 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.458 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.458 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.457 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.457 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.457 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.456 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.456 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.455 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.455 | |
| 2ycr | HCW | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.454 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.454 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.453 | |
| 1osv | CHC | Bile acid receptor | / | 0.453 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.453 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.453 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.452 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.452 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.451 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.451 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.451 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.451 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.450 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.450 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.450 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.449 | |
| 2wmu | ZYU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.449 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.449 | |
| 1me8 | RVP | Inosine-5'-monophosphate dehydrogenase | / | 0.448 | |
| 2yit | YIT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.448 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.448 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.448 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.447 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1ppj | ANY | Cytochrome b | / | 0.447 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.447 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.447 | |
| 1c3e | NHR | Phosphoribosylglycinamide formyltransferase | / | 0.446 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.446 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.446 | |
| 3w78 | CBD | FMN-dependent NADH-azoreductase | / | 0.446 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 4ijp | 1EH | Serine/threonine-protein kinase PRP4 homolog | 2.7.11.1 | 0.446 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.446 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.446 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.445 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.445 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.445 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.445 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.445 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.445 | |
| 3aox | EMH | ALK tyrosine kinase receptor | 2.7.10.1 | 0.445 | |
| 4bdh | WVI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.445 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.444 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.444 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1pox | FAD | Pyruvate oxidase | 1.2.3.3 | 0.443 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.443 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.443 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.442 | |
| 2i0d | MUT | Protease | / | 0.442 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.442 | |
| 3zon | IK1 | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.442 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 5a3b | APR | SIR2 family protein | / | 0.442 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.441 | |
| 2d1c | NAP | Isocitrate dehydrogenase [NADP] | 1.1.1.42 | 0.441 | |
| 2yir | YIR | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.441 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.441 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.441 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.441 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.440 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.440 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.440 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.440 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.440 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.440 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
| 4ks8 | B49 | Serine/threonine-protein kinase PAK 6 | 2.7.11.1 | 0.440 |