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 |
|---|---|---|---|
| 4loc | BTN | Pyruvate carboxylase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4loc | BTN | Pyruvate carboxylase | / | 1.000 | |
| 4mfe | BTN | Pyruvate carboxylase | / | 0.696 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.526 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.503 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.477 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.475 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2rm2 | W43 | Genome polyprotein | / | 0.464 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.461 | |
| 2rr1 | W8R | Genome polyprotein | / | 0.461 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.460 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.460 | |
| 2rs1 | W84 | Genome polyprotein | / | 0.459 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.459 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.458 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.457 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.456 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3eks | CY9 | Actin-5C | / | 0.455 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.454 | |
| 3elc | F01 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.454 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.454 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.452 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.450 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.450 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.449 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.449 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.448 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.448 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.448 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.448 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.447 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.447 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 3r96 | ACO | MccE protein | / | 0.447 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.446 | |
| 3pft | FMN | Flavin reductase | / | 0.446 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.446 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.446 | |
| 4jkt | 04A | Glutaminase kidney isoform, mitochondrial | 3.5.1.2 | 0.446 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 3pcg | 4HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.445 | |
| 3pcg | 4HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.445 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.444 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.444 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.442 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.442 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.442 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.441 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 3tlc | 7MD | Microcin C7 self-immunity protein MccF | / | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.441 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.441 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.440 |