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 |
|---|---|---|---|
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 1.000 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.658 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.632 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.628 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.619 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.611 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.559 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.558 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.555 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.548 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.495 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.477 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.475 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.473 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.472 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.471 | |
| 4rv9 | SAH | D-mycarose 3-C-methyltransferase | / | 0.471 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.469 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.465 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.465 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.464 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.460 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1xaj | NAD | 3-dehydroquinate synthase | / | 0.458 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.458 | |
| 5env | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.458 | |
| 4b1h | AR6 | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.457 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.456 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.454 | |
| 1p4m | ADP | Riboflavin kinase | 2.7.1.26 | 0.454 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.454 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.454 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.453 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.453 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.453 | |
| 3fpd | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.453 | |
| 2zsc | BTN | Tamavidin2 | / | 0.452 | |
| 4bui | W2E | Tankyrase-2 | 2.4.2.30 | 0.452 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.451 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.451 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.450 | |
| 1swe | BTN | Streptavidin | / | 0.450 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.450 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.449 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.448 | |
| 1swr | BTN | Streptavidin | / | 0.448 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.447 | |
| 5hq8 | SAH | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.447 | |
| 1lke | DOG | Bilin-binding protein | / | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4y1b | NAP | AntE | / | 0.446 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.445 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.445 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.445 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.444 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.444 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.444 | |
| 2rto | IMI | Streptavidin | / | 0.443 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3arv | SAU | Chitinase A | / | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 5je3 | SAH | Methyl transferase | / | 0.443 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.442 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3oe5 | 611 | Catechol O-methyltransferase | 2.1.1.6 | 0.441 | |
| 1srf | MTB | Streptavidin | / | 0.440 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 2uyw | BTN | Avd protein | / | 0.440 | |
| 4b1i | A8P | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.440 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |