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 |
|---|---|---|---|
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 1.043 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 1.002 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.952 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.866 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.847 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.815 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.804 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.802 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.795 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.794 | |
| 5je2 | SAH | Methyl transferase | / | 0.784 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.779 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.776 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.774 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.771 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.763 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.762 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.761 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.761 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.759 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.756 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.755 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.753 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.752 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.751 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.750 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.749 | |
| 5je3 | SAH | Methyl transferase | / | 0.747 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.743 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.742 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.741 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.738 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.736 | |
| 3lst | SAH | CalO1 | / | 0.736 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.732 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.729 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.725 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.724 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.720 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.718 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.717 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.716 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.714 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.714 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.714 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.713 | |
| 5epe | SAH | Uncharacterized protein | / | 0.712 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.711 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.710 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.709 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.708 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.708 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.708 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.708 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.706 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.706 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.705 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.701 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.701 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.700 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.698 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.697 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.696 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.695 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.695 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.694 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.693 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.693 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.691 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.691 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.691 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.690 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.689 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.687 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.687 | |
| 4e2x | SAH | Methyltransferase | / | 0.686 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.685 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.685 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.684 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.683 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.683 | |
| 5jdz | SAH | Methyl transferase | / | 0.683 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.682 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.682 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.681 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.680 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.680 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.680 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.680 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.680 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.679 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.679 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.678 | |
| 3p2k | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.678 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.677 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.676 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.676 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.675 | |
| 2cdu | ADP | NADH oxidase | / | 0.675 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.675 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.674 | |
| 4x3q | SAH | SibL | / | 0.674 | |
| 4hh4 | SAH | CcbJ | / | 0.673 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.672 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.672 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.670 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.670 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.670 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.669 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.669 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.668 | |
| 4kvz | SAH | PtnL protein | / | 0.668 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.667 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.667 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.667 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.665 | |
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.665 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.665 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.665 | |
| 2zif | SAM | Methyltransferase | / | 0.664 | |
| 3abi | NAD | Uncharacterized protein | / | 0.664 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.664 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.664 | |
| 5je4 | SAH | Methyl transferase | / | 0.664 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.662 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.661 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.661 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.661 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.660 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.660 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.660 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.659 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.659 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.659 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.659 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.659 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.658 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.658 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.658 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.658 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.657 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.657 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.657 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.656 | |
| 2jj1 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.655 | |
| 2jj1 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.655 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.654 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.654 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.654 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.653 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 4tm3 | FAD | KtzI | / | 0.652 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.651 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.651 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.651 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.650 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.650 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.650 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.650 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.650 |