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 |
|---|---|---|---|
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 1.083 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.855 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.833 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.761 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.743 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.732 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.728 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.722 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.721 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.720 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.717 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.713 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.712 | |
| 5je2 | SAH | Methyl transferase | / | 0.708 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.707 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.706 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.706 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.702 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.702 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.702 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.700 | |
| 3lst | SAH | CalO1 | / | 0.698 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.698 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.698 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.694 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.694 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.693 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.693 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.691 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.690 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.690 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.686 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.686 | |
| 5je3 | SAH | Methyl transferase | / | 0.685 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.684 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.683 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.683 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.683 | |
| 4e2x | SAH | Methyltransferase | / | 0.683 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.681 | |
| 4hh4 | SAH | CcbJ | / | 0.681 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.680 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.680 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.680 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.679 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.679 | |
| 3c3y | SAH | O-methyltransferase | / | 0.679 | |
| 4x3q | SAH | SibL | / | 0.679 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.679 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.678 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.678 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.677 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.677 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.676 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.674 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.674 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.674 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.674 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.672 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.672 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.671 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.671 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.670 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.670 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.670 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.669 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.669 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.669 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.667 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.667 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.667 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.667 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.666 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.666 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.666 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.666 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.663 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.663 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.662 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.662 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.662 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.662 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.662 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.661 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.661 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.661 | |
| 3cbg | SAH | O-methyltransferase | / | 0.661 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.661 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.660 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.660 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.660 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.660 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.660 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.659 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.659 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.659 | |
| 4gf5 | SAH | CalS11 | / | 0.659 | |
| 5jdz | SAH | Methyl transferase | / | 0.659 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.659 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.658 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.658 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.657 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.657 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.656 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.656 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.655 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.655 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.654 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.654 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.654 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.654 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.654 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.653 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.653 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.653 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.653 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.652 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.652 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.652 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.652 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.652 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.651 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.650 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.650 |