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 |
|---|---|---|---|
| 3u8f | FGM | Ribosome inactivating protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3u8f | FGM | Ribosome inactivating protein | / | 1.000 | |
| 4lwx | MU2 | Ribosome inactivating protein | / | 0.621 | |
| 4jtp | ASC | Ribosome inactivating protein | / | 0.606 | |
| 3qji | MGP | Ribosome inactivating protein | / | 0.590 | |
| 5ilw | URI | Ribosome inactivating protein | / | 0.566 | |
| 4emr | MGP | Ribosome inactivating protein | / | 0.564 | |
| 1mrk | FMC | Ribosome-inactivating protein alpha-trichosanthin | 3.2.2.22 | 0.540 | |
| 4zz6 | CTP | Ribosome inactivating protein | / | 0.521 | |
| 1lpc | CMP | Antiviral protein DAP-30 | 3.2.2.22 | 0.510 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.475 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.475 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.472 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.471 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.465 | |
| 1z5u | CMP | Class B acid phosphatase | / | 0.461 | |
| 1t13 | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | / | 0.460 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.459 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.457 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.456 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.456 | |
| 4d2d | ALA_ALA_ALA | Di-or tripeptide:H+ symporter | / | 0.456 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.455 | |
| 4v0s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.454 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.453 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.453 | |
| 2xda | JPS | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.452 | |
| 3eks | CY9 | Actin-5C | / | 0.452 | |
| 4glx | 0XS | DNA ligase | 6.5.1.2 | 0.452 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.451 | |
| 4jxx | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.450 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.449 | |
| 3eku | CY9 | Actin-5C | / | 0.449 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.448 | |
| 2nr4 | FMN | Conserved protein | / | 0.446 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.446 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.446 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.446 | |
| 1euy | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.445 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.445 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.445 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.445 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.444 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.444 | |
| 1qcj | APT | Antiviral protein I | 3.2.2.22 | 0.443 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.443 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.442 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1ifu | FMC | Ricin | 3.2.2.22 | 0.442 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.442 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.442 | |
| 3hiv | TXN | rRNA N-glycosidase | / | 0.442 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 4lcn | GNG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.442 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.442 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3gb4 | D3M | DdmC | / | 0.441 | |
| 3t4h | MD5 | Alpha-ketoglutarate-dependent dioxygenase AlkB | 1.14.11.33 | 0.441 | |
| 1t4c | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.440 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.440 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.440 |