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 |
---|---|---|---|
5je3 | SAH | Methyl transferase |
PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
---|---|---|---|---|---|
5je3 | SAH | Methyl transferase | / | 1.062 | |
5jdz | SAH | Methyl transferase | / | 1.056 | |
5je2 | SAH | Methyl transferase | / | 0.960 | |
5je4 | SAH | Methyl transferase | / | 0.946 | |
3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.847 | |
2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.845 | |
2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.844 | |
4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.829 | |
4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.828 | |
4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.821 | |
4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.818 | |
5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.813 | |
4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.812 | |
3fri | SAH | 16S rRNA methylase | / | 0.803 | |
3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.797 | |
1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.795 | |
3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.795 | |
5bp9 | SAH | Putative methyltransferase protein | / | 0.794 | |
1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.793 | |
4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.793 | |
2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.791 | |
1ve3 | SAM | Uncharacterized protein | / | 0.789 | |
3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.785 | |
5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.785 | |
2qe6 | SAM | Uncharacterized protein | / | 0.784 | |
5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.783 | |
5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.781 | |
5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.780 | |
5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.778 | |
5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.778 | |
3go4 | SAH | Uncharacterized protein | / | 0.777 | |
3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.777 | |
2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.776 | |
3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.776 | |
3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.776 | |
1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.775 | |
1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.774 | |
2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.774 | |
3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.768 | |
2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.767 | |
4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.767 | |
1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.763 | |
2yqz | SAM | Uncharacterized protein | / | 0.762 | |
3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.762 | |
4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.761 | |
4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.760 | |
4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.758 | |
2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.756 | |
3t7s | SAM | Uncharacterized protein | / | 0.756 | |
4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.756 | |
5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.756 | |
1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.754 | |
3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.752 | |
2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.751 | |
2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.750 | |
3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.749 | |
5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.747 | |
4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.744 | |
3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.743 | |
2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.739 | |
3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.735 | |
3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.735 | |
4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.734 | |
3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.732 | |
1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.728 | |
3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.727 | |
4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.727 | |
3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.725 | |
2gs9 | SAH | Uncharacterized protein | / | 0.724 | |
4yuz | S4M | Spermidine synthase, putative | / | 0.724 | |
4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.723 | |
1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.721 | |
2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.721 | |
2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.718 | |
4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.718 | |
4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.718 | |
3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.717 | |
3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.716 | |
2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.714 | |
2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.714 | |
3ldg | SAH | Uncharacterized protein | / | 0.714 | |
3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.712 | |
3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.710 | |
2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.709 | |
3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.709 | |
4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.709 | |
4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.709 | |
1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.708 | |
1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.708 | |
5epe | SAH | Uncharacterized protein | / | 0.707 | |
2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.706 | |
1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.704 | |
4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.704 | |
4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.702 | |
3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.700 | |
4x3q | SAH | SibL | / | 0.699 | |
1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.698 | |
2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.698 | |
3ldf | SAH | Uncharacterized protein | / | 0.698 | |
5bp7 | SAH | SAM-dependent methyltransferase | / | 0.698 | |
3lst | SAH | CalO1 | / | 0.695 | |
3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.694 | |
4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.694 | |
1x1c | SAH | C-20 methyltransferase | / | 0.693 | |
2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.693 | |
2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.691 | |
4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.691 | |
4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.691 | |
2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.690 | |
4hh4 | SAH | CcbJ | / | 0.690 | |
3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.689 | |
1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.688 | |
2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.688 | |
3dh0 | SAM | Uncharacterized protein | / | 0.688 | |
3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.688 | |
3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.688 | |
1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.687 | |
4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.687 | |
1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.686 | |
4mb2 | ATP | Uncharacterized protein | / | 0.686 | |
1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.685 | |
4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.684 | |
2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.683 | |
5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.683 | |
1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.682 | |
2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.682 | |
3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.682 | |
3ou2 | SAH | SAM-dependent methyltransferase | / | 0.682 | |
1x1b | SAH | C-20 methyltransferase | / | 0.681 | |
3qgz | ADN | Histidine triad nucleotide-binding protein 1 | 3 | 0.681 | |
4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.681 | |
4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.681 | |
4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.680 | |
1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.679 | |
1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.679 | |
2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.679 | |
3e23 | SAM | Uncharacterized protein | / | 0.679 | |
3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.679 | |
3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.679 | |
4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.679 | |
4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.679 | |
5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.678 | |
5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.678 | |
3e8s | SAH | Uncharacterized protein | / | 0.677 | |
3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.677 | |
4dmg | SAM | Uncharacterized protein | / | 0.677 | |
4eqg | A5A | Histidine triad nucleotide-binding protein 1 | 3 | 0.677 | |
4yv0 | S4M | Spermidine synthase, putative | / | 0.677 | |
2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.676 | |
3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.675 | |
1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.674 | |
2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.674 | |
3t7t | SAH | Uncharacterized protein | / | 0.674 | |
4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.674 | |
4kwc | SAH | Methyltransferase domain family | / | 0.674 | |
3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.673 | |
3mj4 | FAD | UDP-galactopyranose mutase | / | 0.673 | |
2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.672 | |
1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.671 | |
1uay | ADN | Oxidoreductase | / | 0.671 | |
1x1a | SAM | C-20 methyltransferase | / | 0.671 | |
2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.670 | |
1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.668 | |
4mo2 | FDA | UDP-galactopyranose mutase | / | 0.668 | |
1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.667 | |
1v5e | FAD | Pyruvate oxidase | / | 0.667 | |
3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.667 | |
5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.667 | |
2f8l | SAM | Lmo1582 protein | / | 0.666 | |
2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.666 | |
1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.665 | |
1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.664 | |
2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.664 | |
4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.664 | |
5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.664 | |
1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
4fr0 | SAM | Arsenic methyltransferase | / | 0.663 | |
1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.662 | |
2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.662 | |
3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.662 | |
4hb9 | FAD | Uncharacterized protein | / | 0.662 | |
4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.662 | |
4tm3 | FAD | KtzI | / | 0.662 | |
5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.662 | |
1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.661 | |
2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.661 | |
1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.660 | |
3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.660 | |
1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.659 | |
1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.658 | |
2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.658 | |
3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.658 | |
4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.658 | |
1u5a | BIK | L-lactate dehydrogenase | 1.1.1.27 | 0.657 | |
2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.657 | |
2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.657 | |
3vyw | SAM | Uncharacterized protein | / | 0.657 | |
4ube | 2FA | Adenosine kinase | 2.7.1.20 | 0.657 | |
1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.656 | |
2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.656 | |
3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.656 | |
4poo | SAM | Putative RNA methylase | / | 0.656 | |
4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.655 | |
3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.654 | |
5f2k | SAH | Uncharacterized protein | / | 0.653 | |
3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.652 | |
4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.652 | |
4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.652 | |
2zgv | ADP | Phosphoglycerate kinase 1 | 2.7.2.3 | 0.651 | |
3fpf | MTA | Uncharacterized protein | / | 0.651 | |
3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.651 | |
3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.651 | |
2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.650 | |
4yac | NAI | C alpha-dehydrogenase | / | 0.650 | |
5f8f | SFG | Possible transcriptional regulatory protein | / | 0.650 |