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 |
|---|---|---|---|
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 1.105 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.951 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.855 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.850 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.778 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.777 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.775 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.765 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.758 | |
| 5je2 | SAH | Methyl transferase | / | 0.758 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.757 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.755 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.752 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.750 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.750 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.747 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.743 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.741 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.741 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.741 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.737 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.736 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.733 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.733 | |
| 4x3q | SAH | SibL | / | 0.731 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.730 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.729 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.728 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.725 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.724 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.723 | |
| 4hh4 | SAH | CcbJ | / | 0.723 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.722 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.720 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.719 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.719 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.719 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.718 | |
| 3c3y | SAH | O-methyltransferase | / | 0.718 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.718 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.717 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.717 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.717 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.713 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.711 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.710 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.710 | |
| 5jdz | SAH | Methyl transferase | / | 0.710 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.709 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.709 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.708 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.706 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.705 | |
| 4gf5 | SAH | CalS11 | / | 0.705 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.705 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.704 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.704 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.704 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.704 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.703 | |
| 5je4 | SAH | Methyl transferase | / | 0.703 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.702 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.695 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.695 | |
| 4e2x | SAH | Methyltransferase | / | 0.695 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.693 | |
| 3tos | SAH | CalS11 | / | 0.693 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.693 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.692 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.691 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.691 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.691 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.690 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.690 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.690 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.690 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.690 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.690 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.690 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.690 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.689 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.689 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.689 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.689 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.688 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.688 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.688 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.687 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.687 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.687 | |
| 5je3 | SAH | Methyl transferase | / | 0.687 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.684 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.683 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.683 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.682 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.681 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.680 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.679 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.679 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.679 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.678 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.677 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.677 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.677 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.677 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.676 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.676 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.675 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.675 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.675 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.675 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.674 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.674 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.674 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.673 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.673 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.673 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.673 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.672 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.672 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.671 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.670 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.669 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.669 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.668 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.668 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.668 | |
| 5epe | SAH | Uncharacterized protein | / | 0.668 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.665 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.665 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.663 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.663 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.663 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.663 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.663 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.662 | |
| 3lst | SAH | CalO1 | / | 0.661 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.661 | |
| 1p1b | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.660 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.660 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.660 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.659 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.656 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.656 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.653 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.653 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.653 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.652 |