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 Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.996 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.777 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.736 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.723 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.722 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.719 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.712 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.710 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.707 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.700 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.696 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.696 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.695 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.691 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.690 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.690 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.690 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.690 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.690 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.686 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.686 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.685 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.685 | |
| 4kvz | SAH | PtnL protein | / | 0.683 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.682 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.681 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.680 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.680 | |
| 3tos | SAH | CalS11 | / | 0.677 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.675 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.674 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.674 | |
| 3wv7 | ADP | Hmd co-occurring protein HcgE | / | 0.673 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.673 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.672 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.672 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.669 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.668 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.668 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.667 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.667 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.667 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.666 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.665 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.665 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.664 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.663 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.663 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.662 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.662 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.661 | |
| 4gf5 | SAH | CalS11 | / | 0.661 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.660 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.659 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.659 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.658 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.655 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.655 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.655 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.654 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.653 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.652 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.651 | |
| 4x3q | SAH | SibL | / | 0.651 |