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 |
|---|---|---|---|
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 1.091 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.938 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.774 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.754 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.740 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.734 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.729 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.725 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.723 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.720 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.718 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.717 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.715 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.713 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.712 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.710 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.710 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.710 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.709 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.709 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.707 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.706 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.706 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.705 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.704 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.704 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.704 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.702 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.701 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.701 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.700 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.698 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.696 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.695 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.694 | |
| 4gf5 | SAH | CalS11 | / | 0.693 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.692 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.692 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.691 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.691 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.689 | |
| 4hh4 | SAH | CcbJ | / | 0.688 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.688 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.687 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.686 | |
| 4kvz | SAH | PtnL protein | / | 0.686 | |
| 2cww | SAH | Uncharacterized protein | / | 0.685 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.684 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.683 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.682 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.681 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.679 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.679 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.679 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.679 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.677 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.676 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.674 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.674 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.672 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.672 | |
| 5epe | SAH | Uncharacterized protein | / | 0.672 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.671 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.670 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.669 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.669 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.669 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.668 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.667 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.666 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.666 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.666 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.666 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.666 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.665 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.664 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.664 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.664 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.664 | |
| 4e2x | SAH | Methyltransferase | / | 0.664 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.664 | |
| 3cbg | SAH | O-methyltransferase | / | 0.663 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.662 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.661 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.661 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.661 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.660 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.660 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.660 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.660 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.660 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.660 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.660 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.660 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.659 | |
| 4poo | SAM | Putative RNA methylase | / | 0.659 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.659 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.658 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.656 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.656 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.656 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.656 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.655 | |
| 3tos | SAH | CalS11 | / | 0.655 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.655 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.655 | |
| 5jdz | SAH | Methyl transferase | / | 0.654 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.653 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.653 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.652 | |
| 3emd | SFG | Methyltransferase | / | 0.650 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.650 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.650 | |
| 5je4 | SAH | Methyl transferase | / | 0.650 |