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 |
|---|---|---|---|
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 1.168 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 1.121 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.965 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.759 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.753 | |
| 3tos | SAH | CalS11 | / | 0.744 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.735 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.734 | |
| 4kvz | SAH | PtnL protein | / | 0.728 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.726 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.719 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.718 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.717 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.714 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.714 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.713 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.713 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.712 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.711 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.710 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.706 | |
| 3c3y | SAH | O-methyltransferase | / | 0.706 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.703 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.703 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.699 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.698 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.698 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.697 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.695 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.694 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.694 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.694 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.693 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.693 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.692 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.692 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.690 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.690 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.689 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.689 | |
| 3lst | SAH | CalO1 | / | 0.689 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.688 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.688 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.688 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.688 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.687 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.686 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.685 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.685 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.684 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.684 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.684 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.684 | |
| 4gf5 | SAH | CalS11 | / | 0.682 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.681 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.681 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.680 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.680 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.680 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.679 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.679 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.678 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.678 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.677 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.675 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.674 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.674 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.674 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.673 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.673 | |
| 4hh4 | SAH | CcbJ | / | 0.673 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.673 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.672 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.671 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.670 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.668 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.668 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.668 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.667 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.667 | |
| 5je2 | SAH | Methyl transferase | / | 0.667 | |
| 4ube | 2FA | Adenosine kinase | 2.7.1.20 | 0.666 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.665 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.663 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.662 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.662 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.661 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.661 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.661 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.661 | |
| 5epe | SAH | Uncharacterized protein | / | 0.661 | |
| 2cdu | ADP | NADH oxidase | / | 0.659 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.659 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.659 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.659 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.659 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.658 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.658 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.658 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.657 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.657 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.657 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.657 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.657 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.657 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.656 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.655 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.655 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.655 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.654 | |
| 3r9f | GSU | MccE protein | / | 0.654 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.654 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.654 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.653 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.653 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.653 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.652 | |
| 4e2x | SAH | Methyltransferase | / | 0.652 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.652 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.651 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.650 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.650 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.650 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.650 |