sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2vxk | COA | Glucosamine 6-phosphate acetyltransferase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2vxk | COA | Glucosamine 6-phosphate acetyltransferase, putative | / | 1.000 | |
| 1i12 | ACO | Glucosamine 6-phosphate N-acetyltransferase | / | 0.564 | |
| 2vez | ACO | Glucosamine 6-phosphate acetyltransferase, putative | / | 0.563 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.506 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.504 | |
| 2cy2 | ACO | Probable acetyltransferase | / | 0.500 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.500 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.498 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.494 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.491 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.490 | |
| 4mk9 | 28R | Genome polyprotein | 2.7.7.48 | 0.488 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.487 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.487 | |
| 4phl | PIL | Phosphodiesterase | / | 0.487 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.485 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.484 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.482 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.481 | |
| 3g86 | T18 | Genome polyprotein | 2.7.7.48 | 0.481 | |
| 3h59 | H59 | Genome polyprotein | 2.7.7.48 | 0.480 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.480 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.479 | |
| 3hkw | IX6 | Genome polyprotein | 2.7.7.48 | 0.479 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.478 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.477 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.475 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.474 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.473 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.472 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.471 | |
| 3igv | B80 | Genome polyprotein | 2.7.7.48 | 0.471 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.471 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.471 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.471 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.470 | |
| 3hky | IX6 | Genome polyprotein | 2.7.7.48 | 0.470 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.469 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.469 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.468 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.468 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.467 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.467 | |
| 2jdc | CAO | Probable acetyltransferase | / | 0.466 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.465 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.464 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.464 | |
| 3tyv | HI3 | Genome polyprotein | 2.7.7.48 | 0.463 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.462 | |
| 4j7h | TRH | PCZA361.3 | / | 0.462 | |
| 4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.462 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.462 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.460 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.460 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.460 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.460 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.458 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.458 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.457 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.457 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.457 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.455 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.455 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.454 | |
| 4e2b | FMN | Dehydrogenase | / | 0.454 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.453 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 4ag9 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.452 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.452 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.451 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.450 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.448 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.448 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.447 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.446 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 1pua | COA | HAT A1 | / | 0.445 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.445 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.445 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.445 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.445 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.444 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.444 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 5kgj | ACO | Predicted acetyltransferase | / | 0.444 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.443 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.443 | |
| 3e4a | QIX | Insulin-degrading enzyme | 3.4.24.56 | 0.443 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.443 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.443 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.442 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.442 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.442 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.442 | |
| 3lu8 | IQX | Serum albumin | / | 0.442 | |
| 4d7e | FAD | Putative lysine-N-oxygenase | / | 0.442 | |
| 1pj7 | FFO | Dimethylglycine oxidase | 1.5.3.10 | 0.441 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 2e48 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.441 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 3bsy | ACO | UDP-N-acetylbacillosamine N-acetyltransferase | 2.3.1.203 | 0.441 | |
| 3gyn | B42 | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.441 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.440 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.440 | |
| 3d28 | B34 | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |