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 |
|---|---|---|---|
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 1.000 | |
| 3euf | BAU | Uridine phosphorylase 1 | / | 0.526 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.510 | |
| 3p0e | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.491 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.485 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.483 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.482 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.482 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.478 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.471 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 4phl | PIL | Phosphodiesterase | / | 0.470 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.469 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.466 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.464 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.463 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.461 | |
| 2ejz | SAH | Diphthine synthase | / | 0.460 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.459 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.457 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.457 | |
| 1tgv | 5UD | Uridine phosphorylase | 2.4.2.3 | 0.456 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.455 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.454 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.454 | |
| 4e2y | JHZ | Methyltransferase | / | 0.454 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.453 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.452 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2bxo | OPB | Serum albumin | / | 0.449 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.448 | |
| 1odj | GMP | Purine nucleoside phosphorylase | / | 0.448 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.448 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.447 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4ogk | THM | Uridine phosphorylase | 2.4.2.3 | 0.446 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.445 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.441 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.440 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 |