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 |
|---|---|---|---|
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 1.000 | |
| 2yoz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.625 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.613 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.601 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.599 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.573 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.560 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.537 | |
| 2ydb | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.528 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.526 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.509 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.490 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.490 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.482 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 4wfr | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.474 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.471 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.469 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.469 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.468 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.467 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.463 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.463 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.461 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.461 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.460 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 1ppj | ANY | Cytochrome b | / | 0.459 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.457 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.457 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.457 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.456 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.455 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.454 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.454 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.454 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.453 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.452 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.451 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.451 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.450 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.449 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.446 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.446 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.445 | |
| 2gmv | PEP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.445 | |
| 2ylx | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.444 | |
| 3eku | CY9 | Actin-5C | / | 0.444 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.443 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.442 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.442 | |
| 3t88 | S0N | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.442 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.442 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.442 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.441 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.441 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.440 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.440 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.440 |