sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4k30 | NLG | N-acetylglutamate synthase, mitochondrial | 2.3.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4k30 | NLG | N-acetylglutamate synthase, mitochondrial | 2.3.1.1 | 1.000 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.477 | |
| 5dp2 | NAP | CurF | / | 0.473 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.472 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.466 | |
| 1ryw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.464 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.463 | |
| 4j7h | TRH | PCZA361.3 | / | 0.460 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.458 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.457 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.455 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.453 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.452 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.452 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.451 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.451 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.450 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.450 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.450 | |
| 1n0s | FLU | Bilin-binding protein | / | 0.449 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 1h69 | ARH | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1r2j | FAD | FkbI | / | 0.445 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.445 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.445 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3arv | SAU | Chitinase A | / | 0.444 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.444 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.443 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.443 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.440 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.440 |