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 |
|---|---|---|---|
| 3cbg | SAH | O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3cbg | SAH | O-methyltransferase | / | 1.057 | |
| 3c3y | SAH | O-methyltransferase | / | 0.886 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.859 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.845 | |
| 3tos | SAH | CalS11 | / | 0.842 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.825 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.808 | |
| 4gf5 | SAH | CalS11 | / | 0.800 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.800 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.793 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.779 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.777 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.773 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.770 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.767 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.734 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.726 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.725 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.725 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.722 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.718 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.716 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.716 | |
| 4kvz | SAH | PtnL protein | / | 0.715 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.714 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.714 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.713 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.713 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.712 | |
| 2cww | SAH | Uncharacterized protein | / | 0.710 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.710 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.709 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.707 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.707 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.707 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.707 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.707 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.706 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.705 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.705 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.704 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.703 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.703 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.702 | |
| 3lkz | SFG | Genome polyprotein | / | 0.699 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.699 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.698 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.698 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.696 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.695 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.695 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.694 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.694 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.694 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.693 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.693 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.692 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.692 | |
| 5jdz | SAH | Methyl transferase | / | 0.691 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.690 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.690 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.690 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.689 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.688 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.688 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.687 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.687 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.687 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.686 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.686 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.685 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.685 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.685 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.684 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.683 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.683 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.682 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.682 | |
| 3emd | SFG | Methyltransferase | / | 0.682 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.682 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.681 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.680 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.680 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.679 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.679 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.678 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.677 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.677 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.677 | |
| 4ctk | SAM | Genome polyprotein | / | 0.677 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.677 | |
| 3hvi | 619 | Catechol O-methyltransferase | 2.1.1.6 | 0.675 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.675 | |
| 5je2 | SAH | Methyl transferase | / | 0.675 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.674 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.673 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.673 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.673 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.672 | |
| 2zif | SAM | Methyltransferase | / | 0.672 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.672 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.671 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.671 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.671 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.670 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.670 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.669 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.669 | |
| 1p1b | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.668 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.668 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.668 | |
| 3eey | SAM | rRNA methylase | / | 0.668 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.668 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.667 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.667 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.666 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.666 | |
| 4ctj | SAM | Genome polyprotein | / | 0.666 | |
| 4k6m | SAH | Genome polyprotein | / | 0.666 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.666 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.666 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.665 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.665 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.665 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.665 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.663 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.663 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.663 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.663 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.662 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.662 | |
| 3m6v | SAM | Ribosomal RNA small subunit methyltransferase F | / | 0.662 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.661 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.661 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.661 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.660 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.659 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.659 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.657 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.657 | |
| 5jjr | SAH | Genome polyprotein | / | 0.657 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.656 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.656 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.655 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.655 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.655 | |
| 4egu | 5GP | Putative histidine triad (HIT) protein | / | 0.655 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.655 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.654 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.654 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.654 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.654 | |
| 3lby | SAH | Uncharacterized protein | / | 0.654 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.654 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.653 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.653 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.653 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.652 | |
| 3lst | SAH | CalO1 | / | 0.651 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.651 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.650 |