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 |
|---|---|---|---|
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 1.083 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.844 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.839 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.781 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.761 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.751 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.750 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.745 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.736 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.736 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.733 | |
| 4hh4 | SAH | CcbJ | / | 0.733 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.732 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.731 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.730 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.730 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.726 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.724 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.723 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.722 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.720 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.719 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.718 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.718 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.718 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.717 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.717 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.717 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.717 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.716 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.716 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.714 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.710 | |
| 4e2x | SAH | Methyltransferase | / | 0.710 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.709 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.706 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.706 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.705 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.705 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.704 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.703 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.703 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.701 | |
| 4x3q | SAH | SibL | / | 0.701 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.700 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.699 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.698 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.698 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.697 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.696 | |
| 3lst | SAH | CalO1 | / | 0.695 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.693 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.693 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.693 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.692 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.692 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.690 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.690 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.687 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.685 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.683 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.682 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.682 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.682 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.681 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.680 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.680 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.679 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.679 | |
| 4poo | SAM | Putative RNA methylase | / | 0.679 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.678 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.677 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.677 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.676 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.676 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.676 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.675 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.674 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.673 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.673 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.673 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.672 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.671 | |
| 5je2 | SAH | Methyl transferase | / | 0.671 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.670 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.669 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.669 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.669 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.666 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.666 | |
| 3c3y | SAH | O-methyltransferase | / | 0.666 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.665 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.665 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.665 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.664 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.664 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.662 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.662 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.662 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.662 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.662 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.662 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.662 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.661 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.661 | |
| 5epe | SAH | Uncharacterized protein | / | 0.661 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.659 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.659 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.659 | |
| 3tos | SAH | CalS11 | / | 0.659 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.659 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.659 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.659 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.659 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.658 | |
| 3vaq | ADN | Putative adenosine kinase | / | 0.658 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.657 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.656 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.656 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.656 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.656 | |
| 3emd | SFG | Methyltransferase | / | 0.654 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.654 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.654 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.654 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.654 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.653 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.653 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.653 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.652 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.652 | |
| 3m6w | SAM | Ribosomal RNA small subunit methyltransferase F | / | 0.652 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.651 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.650 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.650 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.650 | |
| 4kvz | SAH | PtnL protein | / | 0.650 |