sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2onz | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2onz | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 1.000 | |
| 2ony | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.710 | |
| 2opb | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.674 | |
| 2obf | F83 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.587 | |
| 2g72 | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.577 | |
| 2g8n | F83 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.556 | |
| 4li8 | 1XQ | Tankyrase-1 | 2.4.2.30 | 0.472 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.471 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.470 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.468 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.465 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.462 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.462 | |
| 2ohh | FMN | Type A flavoprotein FprA | 1 | 0.461 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.460 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.458 | |
| 1olm | VTQ | SEC14-like protein 2 | / | 0.456 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.456 | |
| 3lm4 | HPX | Catechol 2,3-dioxygenase | / | 0.455 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.454 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.454 | |
| 3hz6 | ADP | Xylulokinase | / | 0.453 | |
| 3zv6 | 4HB | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.453 | |
| 4o7u | THF | Thymidylate synthase | / | 0.453 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.452 | |
| 4xzj | NAD | Putative NAD(+)--arginine ADP-ribosyltransferase Vis | 2.4.2.31 | 0.452 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.451 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.451 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.450 | |
| 1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.448 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.447 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.446 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.446 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.446 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.446 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.445 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.445 | |
| 3rga | ILD | Epoxide hydrolase LasB | 5.5.1 | 0.445 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.445 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.445 | |
| 1lcw | SHM | Streptavidin | / | 0.444 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.443 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.443 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.443 | |
| 4kxj | P34 | Nucleoprotein | / | 0.443 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.443 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.442 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.442 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.442 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3ean | NAP | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.442 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.441 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.441 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.440 | |
| 4fc0 | 0T2 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 |