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 |
|---|---|---|---|
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 1.083 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.915 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.896 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.813 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.785 | |
| 4hh4 | SAH | CcbJ | / | 0.767 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.761 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.758 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.756 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.743 | |
| 5je2 | SAH | Methyl transferase | / | 0.740 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.736 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.735 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.732 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.731 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.731 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.729 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.725 | |
| 5jdz | SAH | Methyl transferase | / | 0.725 | |
| 5je3 | SAH | Methyl transferase | / | 0.725 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.721 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.721 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.719 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.718 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.713 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.712 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.711 | |
| 3lst | SAH | CalO1 | / | 0.708 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.707 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.705 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.705 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.705 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.700 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.698 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.697 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.695 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.694 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.694 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.692 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.691 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.690 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.690 | |
| 3ua3 | SAH | Protein arginine N-methyltransferase 5 | / | 0.689 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.688 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.687 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.687 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.687 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.687 | |
| 4x3q | SAH | SibL | / | 0.687 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.686 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.685 | |
| 5je4 | SAH | Methyl transferase | / | 0.685 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.684 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.684 | |
| 3c3y | SAH | O-methyltransferase | / | 0.684 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.683 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.682 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.682 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.681 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.681 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.681 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.679 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.678 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.678 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.678 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.678 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.677 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.677 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.676 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.676 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.675 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.675 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.675 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.675 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.675 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.673 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.673 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.672 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.672 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.671 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.671 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.670 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.670 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.669 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.669 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.669 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.669 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.668 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.668 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.668 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.666 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.664 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.663 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.662 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.661 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.660 | |
| 2oyf | IAC | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.660 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.659 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.658 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.657 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.657 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.656 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.655 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.655 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.654 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.654 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.654 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.654 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.654 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.654 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.653 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.653 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.652 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.652 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.651 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.651 | |
| 3gu3 | SAH | Methyltransferase | / | 0.651 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.651 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.650 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.650 |