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 |
|---|---|---|---|
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 1.139 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.948 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.942 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.859 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.836 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.825 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.815 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.807 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.792 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.779 | |
| 4x3q | SAH | SibL | / | 0.779 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.775 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.769 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.764 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.762 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.760 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.758 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.756 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.755 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.754 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.752 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.751 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.749 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.747 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.747 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.745 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.745 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.745 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.743 | |
| 3lst | SAH | CalO1 | / | 0.741 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.738 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.737 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.736 | |
| 5je2 | SAH | Methyl transferase | / | 0.736 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.735 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.732 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.730 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.726 | |
| 4hh4 | SAH | CcbJ | / | 0.725 | |
| 4e2x | SAH | Methyltransferase | / | 0.724 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.724 | |
| 5epe | SAH | Uncharacterized protein | / | 0.724 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.722 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.722 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.721 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.717 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.716 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.715 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.713 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.713 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.711 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.710 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.709 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.708 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.704 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.703 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.701 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.701 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.700 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.700 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.699 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.697 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.697 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.696 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.695 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.695 | |
| 5jdz | SAH | Methyl transferase | / | 0.695 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.694 | |
| 3c3y | SAH | O-methyltransferase | / | 0.694 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.691 | |
| 3cbg | SAH | O-methyltransferase | / | 0.690 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.689 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.689 | |
| 4kvz | SAH | PtnL protein | / | 0.688 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.688 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.687 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.687 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.686 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.686 | |
| 3lby | SAH | Uncharacterized protein | / | 0.685 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.684 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.684 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.683 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.682 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.682 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.680 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.680 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.679 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.678 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.678 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.677 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.676 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.676 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.676 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.676 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.675 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.672 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.672 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.671 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.671 | |
| 3ua3 | SAH | Protein arginine N-methyltransferase 5 | / | 0.670 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.668 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.666 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.666 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.666 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.665 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.665 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.664 | |
| 5je3 | SAH | Methyl transferase | / | 0.664 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.663 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.663 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.662 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.662 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.662 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.662 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.661 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.660 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.660 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.659 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.659 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.658 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.658 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.656 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.656 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.654 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.653 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.653 | |
| 1p1b | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.652 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.652 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.652 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.651 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.651 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.650 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.650 |