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 |
|---|---|---|---|
| 1eii | RTL | Retinol-binding protein 2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1eii | RTL | Retinol-binding protein 2 | / | 1.000 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.475 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.473 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.472 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.469 | |
| 2f2u | M77 | Rho-associated protein kinase 2 | 2.7.11.1 | 0.467 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.466 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.463 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.462 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.461 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.461 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.460 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.460 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.459 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.458 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.457 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 4phl | PIL | Phosphodiesterase | / | 0.457 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.457 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.456 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.455 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.452 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.452 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.451 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.450 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.450 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.449 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.449 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.449 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.448 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.448 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.448 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.447 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.447 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 4hxy | NDP | Plm1 | / | 0.447 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.447 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.446 | |
| 1t2b | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.446 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.446 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.445 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.445 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4f6w | 0SS | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.445 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.444 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.443 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.442 | |
| 3eku | CY9 | Actin-5C | / | 0.442 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.442 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.441 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 5dhg | DGV | Nociceptin receptor | / | 0.441 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.440 | |
| 4iah | 1DX | Alr2278 protein | / | 0.440 |