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 |
|---|---|---|---|
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 1.000 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.631 | |
| 1mvc | BM6 | Retinoic acid receptor RXR-alpha | / | 0.602 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.600 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.598 | |
| 1xiu | REA | Retinoic acid receptor RXR | / | 0.587 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.579 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.579 | |
| 4m8h | R4M | Retinoic acid receptor RXR-alpha | / | 0.570 | |
| 1xls | REA | Retinoic acid receptor RXR-alpha | / | 0.567 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.565 | |
| 3oap | REA | Retinoic acid receptor RXR-alpha | / | 0.559 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.555 | |
| 4m8e | 29V | Retinoic acid receptor RXR-alpha | / | 0.553 | |
| 1fby | REA | Retinoic acid receptor RXR-alpha | / | 0.552 | |
| 3fal | REA | Retinoic acid receptor RXR-alpha | / | 0.549 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.537 | |
| 3fc6 | REA | Retinoic acid receptor RXR-alpha | / | 0.533 | |
| 2acl | REA | Retinoic acid receptor RXR-alpha | / | 0.531 | |
| 4k4j | 1O8 | Retinoic acid receptor RXR-alpha | / | 0.531 | |
| 1uhl | MEI | Retinoic acid receptor RXR-beta | / | 0.530 | |
| 1fm9 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.529 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.475 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.470 | |
| 3up0 | D7S | aceDAF-12 | / | 0.469 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.466 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.465 | |
| 3gbk | 2PQ | Peroxisome proliferator-activated receptor gamma | / | 0.465 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.464 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.462 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.462 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.461 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.460 | |
| 3q0g | BCO | Probable enoyl-CoA hydratase echA8 | 4.2.1.17 | 0.459 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2xvw | 9NR | Serum albumin | / | 0.458 | |
| 1g3m | PCQ | Estrogen sulfotransferase | 2.8.2.4 | 0.457 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.456 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.455 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.454 | |
| 5bn4 | ANP | V-type ATP synthase alpha chain | / | 0.454 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.451 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.451 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.451 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.450 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.450 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.450 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.449 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 2bxq | IMN | Serum albumin | / | 0.448 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 1ppj | ANY | Cytochrome b | / | 0.447 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.447 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.447 | |
| 2p15 | EZT | Estrogen receptor | / | 0.447 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.447 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.447 | |
| 4klr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 2bxo | OPB | Serum albumin | / | 0.446 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 2wpw | ACO | Orf14 | / | 0.446 | |
| 2x23 | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3b9l | AZZ | Serum albumin | / | 0.446 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.445 | |
| 1fml | RTL | Retinol dehydratase | / | 0.444 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 3i1f | GCP | Translation initiation factor 2 subunit gamma | / | 0.444 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.444 | |
| 3p9t | TCL | Repressor | / | 0.444 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.444 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.444 | |
| 4jvn | YUG | Estrogen sulfotransferase | 2.8.2.4 | 0.443 | |
| 5doz | NDP | JamJ | / | 0.443 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.442 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.442 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.442 | |
| 3wiy | LC6 | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.442 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.441 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.441 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.441 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.440 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.440 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.440 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.440 |