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 |
|---|---|---|---|
| 2vxk | COA | Glucosamine 6-phosphate acetyltransferase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2vxk | COA | Glucosamine 6-phosphate acetyltransferase, putative | / | 1.000 | |
| 2vez | ACO | Glucosamine 6-phosphate acetyltransferase, putative | / | 0.563 | |
| 1i12 | ACO | Glucosamine 6-phosphate N-acetyltransferase | / | 0.540 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.503 | |
| 2cy2 | ACO | Probable acetyltransferase | / | 0.500 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.500 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.498 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.493 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.491 | |
| 2ejz | SAH | Diphthine synthase | / | 0.488 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.485 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.484 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.483 | |
| 4phl | PIL | Phosphodiesterase | / | 0.481 | |
| 4mk7 | 28O | Genome polyprotein | 2.7.7.48 | 0.480 | |
| 3g86 | T18 | Genome polyprotein | 2.7.7.48 | 0.478 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.477 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.477 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.477 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.475 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.475 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.472 | |
| 3h59 | H59 | Genome polyprotein | 2.7.7.48 | 0.472 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.471 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.471 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.470 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.470 | |
| 3hky | IX6 | Genome polyprotein | 2.7.7.48 | 0.470 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.470 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.468 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.467 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.467 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.467 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.465 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.464 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.464 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.464 | |
| 1v5z | 2HC | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.463 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.463 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 4j7h | TRH | PCZA361.3 | / | 0.462 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.461 | |
| 2jdc | CAO | Probable acetyltransferase | / | 0.461 | |
| 4mk9 | 28R | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.460 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.460 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.459 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.458 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.458 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 3ele | PLP | Aminotransferase | / | 0.456 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.456 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.455 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.455 | |
| 3hkw | IX6 | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 3igv | B80 | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.455 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.454 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.454 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.454 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.454 | |
| 4ag9 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.452 | |
| 4el5 | D1M | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.452 | |
| 4ckr | DI1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.451 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.450 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4ih6 | 1EP | Genome polyprotein | 2.7.7.48 | 0.450 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.449 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3e4a | QIX | Insulin-degrading enzyme | 3.4.24.56 | 0.449 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4e2b | FMN | Dehydrogenase | / | 0.449 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.448 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.448 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.448 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.447 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.447 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.447 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.446 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.446 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.446 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.446 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1wp4 | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.445 | |
| 2qe2 | 452 | Polyprotein | / | 0.445 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.445 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.444 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.444 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 3cso | XNI | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.444 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 5kgj | ACO | Predicted acetyltransferase | / | 0.444 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.443 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.442 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.442 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.442 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.442 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.442 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.442 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.441 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.441 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.440 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.440 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.440 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.440 | |
| 4v2g | CTC | Tetracycline repressor protein class D | / | 0.440 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |