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 |
|---|---|---|---|
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 1.007 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.970 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.952 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.875 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.857 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.809 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.798 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.796 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.790 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.788 | |
| 5je3 | SAH | Methyl transferase | / | 0.785 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.784 | |
| 5jdz | SAH | Methyl transferase | / | 0.783 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.778 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.777 | |
| 5je2 | SAH | Methyl transferase | / | 0.776 | |
| 3lst | SAH | CalO1 | / | 0.773 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.772 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.771 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.770 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.767 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.767 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.763 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.759 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.756 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.756 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.755 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.752 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.751 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.751 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.751 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.750 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.745 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.744 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.743 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.742 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.737 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.733 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.733 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.732 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.732 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.731 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.727 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.724 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.723 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.723 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.720 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.718 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.716 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.716 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.713 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.710 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.708 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.707 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.706 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.706 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.705 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.705 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.704 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.702 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.702 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.700 | |
| 5je4 | SAH | Methyl transferase | / | 0.700 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.699 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.699 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.699 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.698 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.698 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.697 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.696 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.696 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.696 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.696 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.695 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.694 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.693 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.693 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.692 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.692 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.692 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.692 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.691 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.689 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.688 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.687 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.686 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.685 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.685 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.685 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.684 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.683 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.683 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.683 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.683 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.683 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.683 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.682 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.681 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.680 | |
| 4x3q | SAH | SibL | / | 0.679 | |
| 5epe | SAH | Uncharacterized protein | / | 0.679 | |
| 3qgz | ADN | Histidine triad nucleotide-binding protein 1 | 3 | 0.678 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.678 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.675 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.675 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.675 | |
| 4tlx | FDA | KtzI | / | 0.675 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.674 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.674 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.673 | |
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.672 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.672 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.672 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.672 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.672 | |
| 3cbg | SAH | O-methyltransferase | / | 0.671 | |
| 4hh4 | SAH | CcbJ | / | 0.671 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.670 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.670 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.670 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.669 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.669 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.669 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.669 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.669 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.668 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.668 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.668 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.668 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.667 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.667 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.667 | |
| 4e2x | SAH | Methyltransferase | / | 0.667 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.666 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.666 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.666 | |
| 3gu3 | SAH | Methyltransferase | / | 0.665 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.665 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.665 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.665 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.664 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.664 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.664 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.663 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.663 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.662 | |
| 4eqg | A5A | Histidine triad nucleotide-binding protein 1 | 3 | 0.662 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.662 | |
| 4tm3 | FAD | KtzI | / | 0.662 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.661 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.661 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.660 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.660 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.660 | |
| 3wdm | ADN | 4-phosphopantoate--beta-alanine ligase | 6.3.2.36 | 0.659 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.659 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.659 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.658 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.658 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.658 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.658 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.658 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.657 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.657 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.656 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.656 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.656 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.656 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.655 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.655 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.654 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.654 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.654 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.654 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.654 | |
| 5il1 | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.654 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.653 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.653 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.653 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.652 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.652 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.652 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.652 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.652 | |
| 3r6t | LU1 | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.651 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.651 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.651 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.650 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.650 |