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 |
|---|---|---|---|
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.978 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.957 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.875 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.866 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.824 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.815 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.805 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.791 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.786 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.785 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.779 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.774 | |
| 3lst | SAH | CalO1 | / | 0.769 | |
| 5je3 | SAH | Methyl transferase | / | 0.768 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.766 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.765 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.764 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.762 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.761 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.759 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.758 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.757 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.757 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.757 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.756 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.751 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.750 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.750 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.749 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.748 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.747 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.746 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.744 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.744 | |
| 5je2 | SAH | Methyl transferase | / | 0.744 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.738 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.738 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.737 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.733 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.732 | |
| 4kvz | SAH | PtnL protein | / | 0.732 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.730 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.726 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.724 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.724 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.719 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.719 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.718 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.716 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.715 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.714 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.713 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.713 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.711 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.710 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.710 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.710 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.709 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.706 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.705 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.703 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.703 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.702 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.702 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.702 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.701 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.701 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.701 | |
| 4hh4 | SAH | CcbJ | / | 0.701 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.698 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.696 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.694 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.692 | |
| 4e2x | SAH | Methyltransferase | / | 0.692 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.692 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.691 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.690 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.690 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.690 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.686 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.686 | |
| 5jdz | SAH | Methyl transferase | / | 0.685 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.684 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.684 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.684 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.683 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.683 | |
| 2zif | SAM | Methyltransferase | / | 0.682 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.681 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.681 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.680 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.679 | |
| 5epe | SAH | Uncharacterized protein | / | 0.679 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.678 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.677 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.676 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.676 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.676 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.675 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.675 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.674 | |
| 2fkn | NAD | Urocanate hydratase | 4.2.1.49 | 0.674 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.674 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.673 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.673 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.673 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.673 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.672 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.672 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.671 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.671 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.671 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.670 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.670 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.668 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.667 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.664 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.664 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.664 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.662 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.661 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.661 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.661 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.660 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.660 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.660 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.660 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.658 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.657 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.657 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.657 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.657 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.657 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.656 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.656 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.655 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.654 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.654 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.653 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 3eey | SAM | rRNA methylase | / | 0.653 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.653 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.652 | |
| 3fpb | ATP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.652 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.652 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.651 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.651 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.651 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.651 | |
| 4x3q | SAH | SibL | / | 0.651 | |
| 3gu3 | SAH | Methyltransferase | / | 0.650 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.650 | |
| 4tlx | FDA | KtzI | / | 0.650 |