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 |
|---|---|---|---|
| 2bsx | NOS | Purine nucleoside phosphorylase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 1.000 | |
| 1pr1 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.561 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.556 | |
| 1pk9 | 2FA | Purine nucleoside phosphorylase DeoD-type | / | 0.555 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.548 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.548 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.543 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.531 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.523 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.517 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.512 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.511 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.509 | |
| 1q1g | MTI | Purine nucleoside phosphorylase | / | 0.508 | |
| 4da0 | GNG | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.505 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.505 | |
| 1nw4 | IMH | Purine nucleoside phosphorylase | / | 0.496 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.495 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.492 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.491 | |
| 4tta | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.483 | |
| 4tti | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.477 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.474 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.474 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.473 | |
| 1a69 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.472 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.472 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.470 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.470 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.465 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.464 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.464 | |
| 3phc | IM5 | Purine nucleoside phosphorylase | / | 0.464 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.462 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.461 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.461 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.459 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.458 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.458 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.456 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.456 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.455 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.455 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.454 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.454 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.453 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.453 | |
| 1c7o | PPG | Hemolysin | / | 0.452 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.450 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.450 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.450 | |
| 3l9m | L9M | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1v48 | HA1 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.447 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.447 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.446 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.445 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.445 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4ts9 | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.445 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.443 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.443 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.441 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.441 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.440 |