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 |
|---|---|---|---|
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 1.130 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.844 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.825 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.758 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.757 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.751 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.749 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.743 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.741 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.739 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.738 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.736 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.732 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.726 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.724 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.724 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.724 | |
| 4x3q | SAH | SibL | / | 0.719 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.719 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.718 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.718 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.715 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.714 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.711 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.710 | |
| 4e2x | SAH | Methyltransferase | / | 0.709 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.708 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.708 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.707 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.705 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.705 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.704 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.703 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.699 | |
| 5epe | SAH | Uncharacterized protein | / | 0.698 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.697 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.697 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.697 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.695 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.695 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.694 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.694 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.693 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.692 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.692 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.690 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.690 | |
| 5je2 | SAH | Methyl transferase | / | 0.689 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.688 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.688 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.687 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.687 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.686 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.686 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.685 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.685 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.685 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.685 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.685 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.685 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.683 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.683 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.681 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.680 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.680 | |
| 3c3y | SAH | O-methyltransferase | / | 0.680 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.680 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.680 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.680 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.679 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.679 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.679 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.678 | |
| 4hh4 | SAH | CcbJ | / | 0.678 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.677 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.676 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.676 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.674 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.674 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.673 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.673 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.671 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.671 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.670 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.670 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.669 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.669 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.668 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.668 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.668 | |
| 4kvz | SAH | PtnL protein | / | 0.667 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.666 | |
| 2zif | SAM | Methyltransferase | / | 0.666 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.665 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.665 | |
| 3lst | SAH | CalO1 | / | 0.665 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.664 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.663 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.663 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.663 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.663 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.663 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.662 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.662 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.661 | |
| 3cbg | SAH | O-methyltransferase | / | 0.661 | |
| 2cww | SAH | Uncharacterized protein | / | 0.660 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.660 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.659 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.659 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.658 | |
| 5je3 | SAH | Methyl transferase | / | 0.658 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.657 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.657 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.656 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.656 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.656 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.656 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.656 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.655 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.655 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.655 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.654 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.654 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.654 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.654 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.654 | |
| 5jdz | SAH | Methyl transferase | / | 0.654 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.653 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.653 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.653 | |
| 3vaq | ADN | Putative adenosine kinase | / | 0.653 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.653 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.653 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.652 | |
| 3zid | GDP | Tubulin-like protein CetZ | / | 0.652 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.652 | |
| 2pkm | ADN | Adenosine kinase | 2.7.1.20 | 0.651 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.651 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.651 | |
| 5je4 | SAH | Methyl transferase | / | 0.651 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.650 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.650 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.650 |