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 |
|---|---|---|---|
| 4da0 | GNG | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4da0 | GNG | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 1.000 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.629 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.618 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.605 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.573 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.567 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.567 | |
| 1pr1 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.546 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.542 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.538 | |
| 1pk9 | 2FA | Purine nucleoside phosphorylase DeoD-type | / | 0.532 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.530 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.528 | |
| 4ts9 | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.527 | |
| 2i4t | UA2 | Purine nucleoside phosphorylase, putative | / | 0.522 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.510 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.509 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.507 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.505 | |
| 1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.504 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.503 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.496 | |
| 1a69 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.494 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.488 | |
| 4tti | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.481 | |
| 4tta | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.480 | |
| 1nw4 | IMH | Purine nucleoside phosphorylase | / | 0.475 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.475 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.472 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.471 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.465 | |
| 5dp2 | NAP | CurF | / | 0.465 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.464 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.463 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.462 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.461 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.459 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.459 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.459 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.458 | |
| 1tys | DHF | Thymidylate synthase | / | 0.457 | |
| 1k9s | FM2 | Purine nucleoside phosphorylase DeoD-type | / | 0.455 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.455 | |
| 1q1g | MTI | Purine nucleoside phosphorylase | / | 0.454 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.453 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3of3 | DIH | Purine nucleoside phosphorylase DeoD-type 1 | / | 0.451 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.451 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.450 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4ktf | 1TM | Cytochrome P450 | / | 0.450 | |
| 5dld | UD1 | UDP-N-Acetylglucosamine 2-epimerase | / | 0.450 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3u4r | 08F | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.445 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.445 | |
| 3phc | IM5 | Purine nucleoside phosphorylase | / | 0.445 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.444 | |
| 5epo | TUD | 7-alpha-hydroxysteroid deydrogenase | / | 0.444 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.443 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.443 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.443 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1c7o | PPG | Hemolysin | / | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1vrq | FON | Subunit alpha of sarocosine oxidase | / | 0.442 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3o3n | IRC | (R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit | / | 0.441 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.441 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.441 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.440 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.440 |