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 |
|---|---|---|---|
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 1.257 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 1.245 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.226 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.205 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 1.185 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 1.154 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 1.132 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 1.109 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 1.100 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.930 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.926 | |
| 5je2 | SAH | Methyl transferase | / | 0.880 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.872 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.862 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.862 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.861 | |
| 4hh4 | SAH | CcbJ | / | 0.841 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.821 | |
| 5je3 | SAH | Methyl transferase | / | 0.813 | |
| 5jdz | SAH | Methyl transferase | / | 0.811 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.806 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.794 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.791 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.790 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.785 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.778 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.778 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.776 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.775 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.774 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.769 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.768 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.768 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.766 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.765 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.764 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.764 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.761 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.760 | |
| 5je4 | SAH | Methyl transferase | / | 0.760 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.759 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.757 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.756 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.750 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.750 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.749 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.748 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.745 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.744 | |
| 4e2x | SAH | Methyltransferase | / | 0.743 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.742 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.741 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.741 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.741 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.740 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.740 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.740 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.740 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.739 | |
| 5epe | SAH | Uncharacterized protein | / | 0.738 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.737 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.735 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.735 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.733 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.731 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.730 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.730 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.728 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.727 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.727 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.726 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.726 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.726 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.723 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.722 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.721 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.721 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.720 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.720 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.717 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.716 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.715 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.715 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.715 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.715 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.713 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.713 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.712 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.711 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.711 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.710 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.710 | |
| 3c3y | SAH | O-methyltransferase | / | 0.709 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.709 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.707 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.706 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.705 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.702 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.702 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.701 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.700 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.700 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.700 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.700 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.697 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.697 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.696 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.696 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.695 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.694 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.694 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.693 | |
| 3lby | SAH | Uncharacterized protein | / | 0.693 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.691 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.691 | |
| 3tos | SAH | CalS11 | / | 0.691 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.691 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.690 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.689 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.686 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.685 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.683 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.682 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.681 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.680 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.679 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.679 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.678 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.678 | |
| 4kvz | SAH | PtnL protein | / | 0.678 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.677 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.677 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.676 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.675 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.675 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.675 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.675 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.675 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.674 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.674 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.674 | |
| 1txz | APR | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.673 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.673 | |
| 2h39 | ADQ | ADP-glucose phosphorylase | / | 0.673 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.673 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.673 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.672 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.672 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.672 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.671 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.671 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.669 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.667 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.666 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.666 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.666 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.664 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.663 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.662 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.662 | |
| 3lst | SAH | CalO1 | / | 0.662 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.662 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.662 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.661 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.661 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.661 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.660 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.660 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.659 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.659 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.658 | |
| 2zbp | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.657 | |
| 3emd | SFG | Methyltransferase | / | 0.657 | |
| 2uxx | FAJ | Lysine-specific histone demethylase 1A | 1 | 0.656 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.655 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.655 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.654 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.652 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.652 | |
| 3lkz | SFG | Genome polyprotein | / | 0.652 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.651 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.651 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.651 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.651 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.650 | |
| 5ahk | FAD | Acetolactate synthase II, large subunit | / | 0.650 |