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 |
|---|---|---|---|
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 1.000 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.686 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.664 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.627 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.618 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.612 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.595 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.578 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.551 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.526 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.507 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.504 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.490 | |
| 2zsc | BTN | Tamavidin2 | / | 0.478 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.478 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.471 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.470 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.467 | |
| 1lke | DOG | Bilin-binding protein | / | 0.466 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.465 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.463 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.462 | |
| 1g28 | FMN | PHY3 | / | 0.461 | |
| 2egs | SAH | Diphthine synthase | / | 0.461 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.460 | |
| 1p4m | ADP | Riboflavin kinase | 2.7.1.26 | 0.459 | |
| 3up0 | D7S | aceDAF-12 | / | 0.459 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.458 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.457 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.457 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.456 | |
| 4e2x | SAH | Methyltransferase | / | 0.455 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.455 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.454 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.454 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.454 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.453 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.453 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.453 | |
| 4y1b | NAP | AntE | / | 0.453 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.452 | |
| 5egh | PC | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | / | 0.452 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.451 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.450 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.450 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.450 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.450 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.449 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.449 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.449 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.449 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.448 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.448 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.448 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.448 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.447 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.447 | |
| 2xlt | NA0 | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.447 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.446 | |
| 3tp0 | FO5 | HTH-type transcriptional regulator EthR | / | 0.446 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.446 | |
| 4b1h | AR6 | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.446 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.446 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.445 | |
| 2e8q | SAH | Diphthine synthase | / | 0.445 | |
| 3up3 | XCA | aceDAF-12 | / | 0.445 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.444 | |
| 2egb | SAH | Diphthine synthase | / | 0.444 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.444 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.444 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.443 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.443 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.443 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.442 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 3t4h | MD5 | Alpha-ketoglutarate-dependent dioxygenase AlkB | 1.14.11.33 | 0.442 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.442 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 5epe | SAH | Uncharacterized protein | / | 0.442 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.441 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2eka | SAH | Diphthine synthase | / | 0.441 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.441 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.441 | |
| 3wv7 | ADP | Hmd co-occurring protein HcgE | / | 0.441 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.440 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2ejk | SAH | Diphthine synthase | / | 0.440 | |
| 2xvh | NAP | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.440 | |
| 3klb | FMN | Uncharacterized protein | / | 0.440 | |
| 4j7h | TRH | PCZA361.3 | / | 0.440 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.440 |