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 |
|---|---|---|---|
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 1.096 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.914 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.867 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.859 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.811 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.781 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.774 | |
| 3lst | SAH | CalO1 | / | 0.772 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.771 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.768 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.762 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.754 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.749 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.744 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.736 | |
| 3tos | SAH | CalS11 | / | 0.734 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.733 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.728 | |
| 5epe | SAH | Uncharacterized protein | / | 0.727 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.725 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.725 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.724 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.724 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.723 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.721 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.720 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.718 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.716 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.714 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.710 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.710 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.710 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.702 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.701 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.700 | |
| 3c3y | SAH | O-methyltransferase | / | 0.699 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.698 | |
| 4gf5 | SAH | CalS11 | / | 0.696 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.695 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.693 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.691 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.691 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.688 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.688 | |
| 4hh4 | SAH | CcbJ | / | 0.688 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.688 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.686 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.684 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.684 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.682 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.682 | |
| 3cbg | SAH | O-methyltransferase | / | 0.680 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.680 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.680 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.680 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.679 | |
| 4e2x | SAH | Methyltransferase | / | 0.679 | |
| 4kvz | SAH | PtnL protein | / | 0.679 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.679 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.679 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.678 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.676 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.676 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.675 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.675 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.674 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.674 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.674 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.673 | |
| 5je2 | SAH | Methyl transferase | / | 0.673 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.672 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.672 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.672 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.669 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.669 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.669 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.669 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.668 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.668 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.667 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.666 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.666 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.666 | |
| 3ua3 | SAH | Protein arginine N-methyltransferase 5 | / | 0.664 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.663 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.663 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.661 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.661 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.661 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.661 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.660 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.660 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.659 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.659 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.658 | |
| 3lby | SAH | Uncharacterized protein | / | 0.658 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.658 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.656 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.656 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.655 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.652 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.652 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.652 | |
| 5je3 | SAH | Methyl transferase | / | 0.652 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.651 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.650 |