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 |
|---|---|---|---|
| 4c03 | SFG | Protein arginine N-methyltransferase 6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 1.291 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.207 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 1.192 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 1.142 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 1.132 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.110 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 1.079 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 1.062 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 1.044 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.990 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.908 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.867 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.853 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.836 | |
| 5je3 | SAH | Methyl transferase | / | 0.829 | |
| 5jdz | SAH | Methyl transferase | / | 0.827 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.818 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.800 | |
| 5je2 | SAH | Methyl transferase | / | 0.798 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.795 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.793 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.790 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.790 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.786 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.782 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.780 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.773 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.767 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.765 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.762 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.761 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.758 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.753 | |
| 4hh4 | SAH | CcbJ | / | 0.752 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.750 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.750 | |
| 5je4 | SAH | Methyl transferase | / | 0.747 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.746 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.745 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.745 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.742 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.740 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.739 | |
| 5epe | SAH | Uncharacterized protein | / | 0.739 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.737 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.736 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.735 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.732 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.732 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.732 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.728 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.728 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.727 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.727 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.723 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.719 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.718 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.717 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.717 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.717 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.715 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.715 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.713 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.711 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.711 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.711 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.710 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.709 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.708 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.707 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.707 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.705 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.705 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.705 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.704 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.704 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.703 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.702 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.702 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.702 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.701 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.700 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.699 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.699 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.699 | |
| 3cbg | SAH | O-methyltransferase | / | 0.698 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.698 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.697 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.695 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.695 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.693 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.692 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.692 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.692 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.692 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.691 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.690 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.690 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.689 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.686 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.686 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.685 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.685 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.684 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.683 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.683 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.683 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.683 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.681 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.681 | |
| 4x3q | SAH | SibL | / | 0.681 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.680 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.680 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.679 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.679 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.678 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.677 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.676 | |
| 3lst | SAH | CalO1 | / | 0.676 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.676 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.675 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.675 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.675 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.675 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.675 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.675 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.675 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.673 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.673 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.673 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.673 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.672 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.672 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.671 | |
| 2v7g | NAD | Urocanate hydratase | 4.2.1.49 | 0.669 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.669 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.668 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.668 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.668 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.667 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.666 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.666 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.666 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.666 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.665 | |
| 3gu3 | SAH | Methyltransferase | / | 0.663 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.662 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.660 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.660 | |
| 2cdu | ADP | NADH oxidase | / | 0.658 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.658 | |
| 4e2x | SAH | Methyltransferase | / | 0.658 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.658 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.657 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.657 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.655 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.654 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.654 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.654 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.654 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.654 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 3eld | SFG | Methyltransferase | / | 0.653 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.653 | |
| 3lby | SAH | Uncharacterized protein | / | 0.652 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.652 | |
| 3alm | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.651 | |
| 3lkz | SFG | Genome polyprotein | / | 0.651 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.650 |