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 |
|---|---|---|---|
| 3i9k | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3i9k | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 1.000 | |
| 2hct | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.518 | |
| 3i9j | NFD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 0.494 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.487 | |
| 3zwx | AV1 | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 0.479 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.471 | |
| 3zwo | G2Q | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 0.469 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.468 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.467 | |
| 3dzj | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.466 | |
| 4kmz | FOL | Folate receptor beta | / | 0.466 | |
| 1a26 | CNA | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.465 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.465 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.462 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.462 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.460 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.460 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.459 | |
| 3hf8 | ML0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.459 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.459 | |
| 4phl | PIL | Phosphodiesterase | / | 0.459 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.457 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4a7y | NHF | Aldos-2-ulose dehydratase | / | 0.457 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.457 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.456 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.456 | |
| 2y4s | BCD | Limit dextrinase | / | 0.456 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.456 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.455 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.455 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.455 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.455 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.453 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.453 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.453 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.452 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4kn1 | 04J | Folate receptor beta | / | 0.452 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.451 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.451 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.451 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.451 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.451 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4rel | KMP | Glycosyltransferase | / | 0.451 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.450 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.450 | |
| 4a7z | AY9 | Aldos-2-ulose dehydratase | / | 0.450 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.449 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.449 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.449 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.449 | |
| 4a16 | H34 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.449 | |
| 1x2e | ATX | Proline iminopeptidase | 3.4.11.5 | 0.448 | |
| 1z5u | CMP | Class B acid phosphatase | / | 0.447 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2gms | P0P | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.447 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 2po3 | T4K | 4-dehydrase | / | 0.447 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.447 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.447 | |
| 4kn0 | MTX | Folate receptor beta | / | 0.447 | |
| 1fml | RTL | Retinol dehydratase | / | 0.446 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.446 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.445 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2wnb | C5P | CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1 | 2.4.99.4 | 0.445 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.445 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 1el4 | CTZ | Obelin | / | 0.444 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.444 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.444 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2fzb | TOL | Aldose reductase | 1.1.1.21 | 0.444 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.444 | |
| 3r43 | ID8 | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.443 | |
| 1s36 | CEI | Obelin | / | 0.443 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.443 | |
| 2j7d | GI1 | Beta-glucosidase A | 3.2.1.21 | 0.443 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.443 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.443 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.443 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4s1h | ADP | Pyridoxal kinase, putative | / | 0.443 | |
| 1frb | ZST | Aldose reductase-related protein 2 | / | 0.442 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.442 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.442 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.442 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.442 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.442 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.441 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.441 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.441 | |
| 2j7c | IDE | Beta-glucosidase A | 3.2.1.21 | 0.441 | |
| 3sfh | 1DI | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 3wd2 | A1L | Chitinase B | 3.2.1.14 | 0.441 | |
| 3wg6 | NDP | NADPH-dependent conjugated polyketone reductase C1 | / | 0.441 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.441 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.441 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.440 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.440 | |
| 3pbl | ETQ | D(3) dopamine receptor | / | 0.440 |