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 |
|---|---|---|---|
| 1sze | 173 | Cytochrome b2, mitochondrial | 1.1.2.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1sze | 173 | Cytochrome b2, mitochondrial | 1.1.2.3 | 1.000 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.487 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.485 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.473 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.471 | |
| 1tys | DHF | Thymidylate synthase | / | 0.469 | |
| 3bhr | THG | Thymidylate synthase | / | 0.468 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.465 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.462 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.461 | |
| 4o7u | THF | Thymidylate synthase | / | 0.461 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.460 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.459 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.459 | |
| 4lsa | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.458 | |
| 1w7k | ADP | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.457 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.457 | |
| 1tdu | DUR | Thymidylate synthase | / | 0.456 | |
| 2fto | TMP | Thymidylate synthase | / | 0.454 | |
| 3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.453 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.453 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.453 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.452 | |
| 4jd3 | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.451 | |
| 4glx | 0XS | DNA ligase | 6.5.1.2 | 0.450 | |
| 3bhl | THG | Thymidylate synthase | / | 0.449 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.448 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.448 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.447 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.447 | |
| 3l5b | BDO | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.447 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.447 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.447 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.446 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.446 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.446 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.445 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4msg | 2C6 | Tankyrase-1 | 2.4.2.30 | 0.445 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1tys | TMP | Thymidylate synthase | / | 0.444 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1dfo | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.443 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.443 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.442 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.441 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.441 | |
| 3bgr | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 4rw6 | 494 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1pt8 | ACO | Formyl-CoA:oxalate CoA-transferase | / | 0.440 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.440 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.440 | |
| 4eil | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4phl | PIL | Phosphodiesterase | / | 0.440 | |
| 5a3b | APR | SIR2 family protein | / | 0.440 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 |