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 |
|---|---|---|---|
| 4qnv | GEK | tRNA U34 carboxymethyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 1.042 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.847 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.723 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.720 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.717 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.710 | |
| 5je2 | SAH | Methyl transferase | / | 0.710 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.709 | |
| 5jdz | SAH | Methyl transferase | / | 0.707 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.704 | |
| 5je3 | SAH | Methyl transferase | / | 0.704 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.702 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.701 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.700 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.697 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.696 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.696 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.693 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.692 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.689 | |
| 4hh4 | SAH | CcbJ | / | 0.687 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.686 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.686 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.682 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.681 | |
| 5epe | SAH | Uncharacterized protein | / | 0.681 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.680 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.680 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.679 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.677 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.674 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.673 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.672 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.672 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.672 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.671 | |
| 4kvz | SAH | PtnL protein | / | 0.670 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.670 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.669 | |
| 4e2x | SAH | Methyltransferase | / | 0.669 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.667 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.667 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.667 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.666 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.666 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.666 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.666 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.666 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.665 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.663 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.663 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.662 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.662 | |
| 2dji | FAD | Pyruvate oxidase | / | 0.661 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.661 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.661 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.661 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.661 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.661 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.660 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.658 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.657 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.657 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.657 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.657 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.657 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.656 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.655 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.654 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.654 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.654 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.653 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.652 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.651 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.651 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.650 |