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 |
|---|---|---|---|
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.308 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 1.283 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.259 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 1.226 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 1.226 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 1.211 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 1.148 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 1.120 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 1.110 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 1.036 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.937 | |
| 5je2 | SAH | Methyl transferase | / | 0.889 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.859 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.858 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.821 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.812 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.808 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.807 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.805 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.805 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.804 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.803 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.796 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.795 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.793 | |
| 4hh4 | SAH | CcbJ | / | 0.784 | |
| 5je3 | SAH | Methyl transferase | / | 0.781 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.780 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.772 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.769 | |
| 5jdz | SAH | Methyl transferase | / | 0.767 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.761 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.758 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.757 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.756 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.755 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.755 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.753 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.752 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.752 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.751 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.750 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.748 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.747 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.744 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.743 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.742 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.739 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.738 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.737 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.736 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.736 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.734 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.732 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.730 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.729 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.729 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.728 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.728 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.727 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.727 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.726 | |
| 5epe | SAH | Uncharacterized protein | / | 0.721 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.720 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.718 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.718 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.716 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.714 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.713 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.712 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.711 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.711 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.709 | |
| 4e2x | SAH | Methyltransferase | / | 0.709 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.708 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.708 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.707 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.707 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.707 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.706 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.706 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.706 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.704 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.703 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.703 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.702 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.701 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.701 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.700 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.700 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.700 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.700 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.698 | |
| 3lst | SAH | CalO1 | / | 0.698 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.698 | |
| 5je4 | SAH | Methyl transferase | / | 0.698 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.697 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.697 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.696 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.696 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.695 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.695 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.694 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.692 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.691 | |
| 4x3q | SAH | SibL | / | 0.691 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.690 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.690 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.689 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.688 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.688 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.685 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.685 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.685 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.685 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.682 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.680 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.680 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.679 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.678 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.678 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.677 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.677 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.676 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.676 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.676 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.675 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.675 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.675 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.674 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.674 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.674 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.674 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.674 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.673 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.671 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.671 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.671 | |
| 3lby | SAH | Uncharacterized protein | / | 0.671 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.671 | |
| 2pkm | ADN | Adenosine kinase | 2.7.1.20 | 0.670 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.669 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.669 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.668 | |
| 2z02 | ATP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 6.3.2.6 | 0.666 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.666 | |
| 3dzi | RGT | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.665 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.665 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.664 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.664 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.663 | |
| 4kvz | SAH | PtnL protein | / | 0.663 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.662 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.662 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.662 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.662 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.662 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.661 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.661 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.661 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.661 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.661 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.661 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.660 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.659 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.659 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.658 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.658 | |
| 3gu3 | SAH | Methyltransferase | / | 0.657 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.657 | |
| 3ua3 | SAH | Protein arginine N-methyltransferase 5 | / | 0.657 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.657 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.656 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.656 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.656 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.654 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.653 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.653 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.653 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.652 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.651 | |
| 1kws | UGA | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3 | / | 0.650 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.650 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.650 |