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 |
|---|---|---|---|
| 4dm6 | TTB | Retinoic acid receptor beta |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4dm6 | TTB | Retinoic acid receptor beta | / | 1.000 | |
| 4dm8 | REA | Retinoic acid receptor beta | / | 0.642 | |
| 2lbd | REA | Retinoic acid receptor gamma | / | 0.635 | |
| 1fd0 | 254 | Retinoic acid receptor gamma | / | 0.625 | |
| 1exa | 394 | Retinoic acid receptor gamma | / | 0.601 | |
| 1xdk | REA | Retinoic acid receptor beta | / | 0.599 | |
| 1fcx | 184 | Retinoic acid receptor gamma | / | 0.576 | |
| 1fcy | 564 | Retinoic acid receptor gamma | / | 0.566 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.498 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.494 | |
| 2bxo | OPB | Serum albumin | / | 0.492 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.489 | |
| 3fmz | 2T1 | Retinol-binding protein 4 | / | 0.487 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.476 | |
| 2cul | FAD | GidA-related protein | / | 0.474 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.473 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.472 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.471 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.470 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.470 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.469 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.469 | |
| 2lf1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.468 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.466 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.465 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.465 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.462 | |
| 3fl9 | TOP | Dihydrofolate reductase | / | 0.462 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.461 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.460 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.460 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.459 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.459 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.458 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.458 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.457 | |
| 3up3 | XCA | aceDAF-12 | / | 0.457 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.457 | |
| 2p15 | EZT | Estrogen receptor | / | 0.456 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.456 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.455 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.455 | |
| 3jq8 | DX3 | Pteridine reductase, putative | / | 0.454 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.454 | |
| 2xkc | 4VQ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.453 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.451 | |
| 4ifv | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.450 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.449 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.448 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.447 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.446 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.446 | |
| 4a6e | ASE | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.446 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.445 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.444 | |
| 2xvv | 9DN | Serum albumin | / | 0.444 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.444 | |
| 4xoq | F42 | Coenzyme F420:L-glutamate ligase | / | 0.444 | |
| 2bo8 | GDX | Mannosylglycerate synthase | / | 0.443 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.443 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.443 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.442 | |
| 2b04 | CHO | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.442 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 1jra | FAD | FAD-linked sulfhydryl oxidase ERV2 | 1.8.3.2 | 0.441 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.441 | |
| 1wsv | THH | Aminomethyltransferase, mitochondrial | / | 0.441 | |
| 3zkp | ERB | Erythromycin C-12 hydroxylase | 1.14.13.154 | 0.441 | |
| 4iah | 1DX | Alr2278 protein | / | 0.441 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.440 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3aba | FLI | Cytochrome P450 | / | 0.440 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.440 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.440 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.440 |