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 |
|---|---|---|---|
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 1.291 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 1.238 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.226 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 1.196 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 1.182 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 1.154 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 1.136 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 1.100 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 1.079 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.919 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.916 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.889 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.861 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.847 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.838 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.815 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.806 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.805 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.803 | |
| 5je2 | SAH | Methyl transferase | / | 0.800 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.798 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.797 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.786 | |
| 5je3 | SAH | Methyl transferase | / | 0.785 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.780 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.779 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.779 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.778 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.778 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.775 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.774 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.771 | |
| 5jdz | SAH | Methyl transferase | / | 0.771 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.766 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.764 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.757 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.753 | |
| 4hh4 | SAH | CcbJ | / | 0.752 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.750 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.747 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.745 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.741 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.741 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.739 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.739 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.739 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.738 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.736 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.735 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.733 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.732 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.730 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.730 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.728 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.727 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.726 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.726 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.725 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.723 | |
| 3lst | SAH | CalO1 | / | 0.722 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.720 | |
| 5je4 | SAH | Methyl transferase | / | 0.720 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.719 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.718 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.718 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.717 | |
| 3c3y | SAH | O-methyltransferase | / | 0.717 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.717 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.716 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.715 | |
| 4e2x | SAH | Methyltransferase | / | 0.715 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.714 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.714 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.714 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.713 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.712 | |
| 3lby | SAH | Uncharacterized protein | / | 0.711 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.711 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.710 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.709 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.705 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.705 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.702 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.702 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.702 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.701 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.701 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.701 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.701 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.700 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.699 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.696 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.696 | |
| 4x3q | SAH | SibL | / | 0.696 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.694 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.693 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.693 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.692 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.691 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.690 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.690 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.690 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.690 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.690 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.689 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.689 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.688 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.688 | |
| 3qgz | ADN | Histidine triad nucleotide-binding protein 1 | 3 | 0.687 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.686 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.686 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.686 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.685 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.685 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.685 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.684 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.684 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.684 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.683 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.682 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.681 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.681 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.680 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.680 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.680 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.680 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.679 | |
| 3cbg | SAH | O-methyltransferase | / | 0.678 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.677 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.677 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.675 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.675 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.675 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.674 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.674 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.674 | |
| 4lv5 | ADP | Rhoptry protein 5B | / | 0.674 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.674 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.673 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.670 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.670 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.669 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.669 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.668 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.668 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.667 | |
| 5epe | SAH | Uncharacterized protein | / | 0.667 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.666 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.665 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.664 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.664 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.664 | |
| 3rfa | SAM | Dual-specificity RNA methyltransferase RlmN | / | 0.664 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.664 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.664 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.663 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.663 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.662 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.662 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.661 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.661 | |
| 3gu3 | SAH | Methyltransferase | / | 0.661 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.661 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.661 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.661 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.660 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.660 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.657 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.657 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.657 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.656 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.656 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.656 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.656 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.656 | |
| 2zif | SAM | Methyltransferase | / | 0.655 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.655 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.654 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.652 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.652 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.651 | |
| 3lct | ADP | ALK tyrosine kinase receptor | 2.7.10.1 | 0.651 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.651 | |
| 1v59 | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.650 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.650 | |
| 3ua3 | SAH | Protein arginine N-methyltransferase 5 | / | 0.650 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.650 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.650 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.650 |