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 |
|---|---|---|---|
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 1.057 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 1.002 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.970 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.957 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.851 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.842 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.838 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.826 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.815 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.815 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.815 | |
| 5je2 | SAH | Methyl transferase | / | 0.812 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.811 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.809 | |
| 3lst | SAH | CalO1 | / | 0.806 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.804 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.798 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.798 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.794 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.794 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.793 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.793 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.790 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.789 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.782 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.779 | |
| 5je3 | SAH | Methyl transferase | / | 0.778 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.775 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.774 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.770 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.770 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.768 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.768 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.764 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.764 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.762 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.759 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.759 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.754 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.753 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.752 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.747 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.744 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.742 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.742 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.742 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.741 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.737 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.735 | |
| 4kvz | SAH | PtnL protein | / | 0.734 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.733 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.732 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.730 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.728 | |
| 5jdz | SAH | Methyl transferase | / | 0.726 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.724 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.724 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.723 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.723 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.723 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.721 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.721 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.721 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.719 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.719 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.719 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.719 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.717 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.717 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.715 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.715 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.714 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.714 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.714 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.713 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.713 | |
| 3cbg | SAH | O-methyltransferase | / | 0.713 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.713 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.713 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.711 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.711 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.710 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.710 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.709 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.709 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.708 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.708 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.707 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.705 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.704 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.704 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.703 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.701 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.700 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.700 | |
| 4hh4 | SAH | CcbJ | / | 0.700 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.700 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.699 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.698 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.698 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.697 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.697 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.695 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.695 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.694 | |
| 4e2x | SAH | Methyltransferase | / | 0.694 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.693 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.693 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.692 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.691 | |
| 3gu3 | SAH | Methyltransferase | / | 0.690 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.690 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.689 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.689 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.689 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.688 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.688 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.688 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.686 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.686 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 3c3y | SAH | O-methyltransferase | / | 0.685 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.684 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.684 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.683 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.683 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.682 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.682 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.681 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.681 | |
| 2zif | SAM | Methyltransferase | / | 0.680 | |
| 4tlx | FDA | KtzI | / | 0.680 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.679 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.679 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.679 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.679 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.678 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.678 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.678 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.678 | |
| 2cdu | ADP | NADH oxidase | / | 0.677 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.676 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.676 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.676 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.675 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.675 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.675 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.675 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.674 | |
| 4icy | FAD | PgaE | / | 0.674 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.673 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.672 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.672 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.671 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.671 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.671 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.670 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.670 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.670 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.669 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.669 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.669 | |
| 3abi | NAD | Uncharacterized protein | / | 0.668 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.668 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.668 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.668 | |
| 5je4 | SAH | Methyl transferase | / | 0.668 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.667 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.666 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.666 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.666 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.665 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.665 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.665 | |
| 4tm3 | FAD | KtzI | / | 0.665 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.664 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.664 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.664 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.664 | |
| 3qgz | ADN | Histidine triad nucleotide-binding protein 1 | 3 | 0.663 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.663 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.663 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.662 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.662 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.662 | |
| 1zk7 | FAD | Mercuric reductase | 1.16.1.1 | 0.660 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.660 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.660 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.660 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.659 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.659 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.659 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.659 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.658 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.658 | |
| 4h0n | SAH | Dnmt2 | / | 0.658 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.658 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.658 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.657 | |
| 4eqe | KAA | Histidine triad nucleotide-binding protein 1 | 3 | 0.657 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.656 | |
| 4bdo | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.656 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.656 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.655 | |
| 4ctk | SAM | Genome polyprotein | / | 0.655 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.655 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.654 | |
| 2uyq | SAM | Putative S-adenosyl-L-methionine-dependent methyltransferase ML2640 | 2.1.1 | 0.654 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.654 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.654 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.653 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.652 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.652 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.652 | |
| 4eqg | A5A | Histidine triad nucleotide-binding protein 1 | 3 | 0.652 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.652 | |
| 2oy0 | SAH | Genome polyprotein | / | 0.651 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.651 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.650 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.650 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.650 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.650 | |
| 5epe | SAH | Uncharacterized protein | / | 0.650 |