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 |
|---|---|---|---|
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 1.000 | |
| 3r9x | GNP | GTPase Era | / | 0.500 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.487 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.486 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.482 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.482 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.480 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.478 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.478 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.478 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.474 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.472 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.472 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.472 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.471 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.471 | |
| 3cx6 | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.469 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.468 | |
| 1okk | GCP | Signal recognition particle protein | / | 0.468 | |
| 1okk | GCP | Signal recognition particle receptor FtsY | / | 0.468 | |
| 2oo7 | AP5 | Adenylate kinase | / | 0.468 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.468 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.468 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.467 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.466 | |
| 1dvr | ATF | Adenylate kinase | / | 0.465 | |
| 3b1x | GNP | Ferrous iron transport protein B | / | 0.464 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.463 | |
| 1e4y | AP5 | Adenylate kinase | / | 0.460 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.460 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.460 | |
| 1svm | ATP | Large T antigen | 3.6.4 | 0.459 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.459 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.456 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.456 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.455 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.454 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.452 | |
| 3jvv | ACP | Twitching mobility protein | / | 0.452 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 3qe0 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.451 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.451 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.451 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 1sxj | AGS | Replication factor C subunit 1 | / | 0.450 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.449 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.448 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.448 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.446 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.445 | |
| 4xvu | ATP | ATPase GET3 | / | 0.445 | |
| 4yvz | 3AT | DNA integrity scanning protein DisA | / | 0.445 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.444 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.444 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.443 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.443 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.443 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1rj9 | GCP | Signal recognition particle receptor FtsY | / | 0.443 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.443 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1kny | APC | Kanamycin nucleotidyltransferase | 2.7.7 | 0.442 | |
| 4v02 | ATP | Site-determining protein | / | 0.442 | |
| 5cyp | GSP | Septin-9 | / | 0.442 | |
| 1zio | AP5 | Adenylate kinase | / | 0.441 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.441 | |
| 2eu8 | AP5 | Adenylate kinase | / | 0.441 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.441 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.441 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.441 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.441 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 4lj9 | ACP | Chaperone protein ClpB | / | 0.441 | |
| 4qbg | AP5 | Adenylate kinase | / | 0.441 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.441 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3ieu | GDP | GTPase Era | / | 0.440 |