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 |
|---|---|---|---|
| 1kmy | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1kmy | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 1.000 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.579 | |
| 1lgt | BP3 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.575 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.520 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.506 | |
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.501 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.491 | |
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.490 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.488 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.487 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.483 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.478 | |
| 4kxj | P34 | Nucleoprotein | / | 0.475 | |
| 3v0m | 5GW | Histo-blood group ABO system transferase | / | 0.473 | |
| 3v0n | 4GW | Histo-blood group ABO system transferase | / | 0.472 | |
| 2jfh | LK1 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.471 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.470 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 4pzr | COA | Histone acetyltransferase p300 | / | 0.468 | |
| 4mzu | TYD | WxcM-like protein | / | 0.466 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.464 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.464 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.462 | |
| 1e2n | RCA | Thymidine kinase | / | 0.462 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.462 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.462 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.462 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.458 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.457 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.457 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.456 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.455 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.454 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.454 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.454 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.453 | |
| 4qak | 2AM | RNA 2',3'-cyclic phosphodiesterase | / | 0.453 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.452 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3ahi | HTL | Probable phosphoketolase | / | 0.451 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.450 | |
| 1eio | GCH | Gastrotropin | / | 0.449 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.448 | |
| 3lnc | 5GP | Guanylate kinase | / | 0.448 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.447 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 4fxf | ATP | Pyruvate kinase PKM | 2.7.1.40 | 0.447 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.446 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2y67 | N21 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.446 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.444 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.443 | |
| 3v2u | ATP | Protein GAL3 | / | 0.443 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.442 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.442 | |
| 3pn1 | IVH | DNA ligase | / | 0.442 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.441 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.441 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.441 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 |