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 |
|---|---|---|---|
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 1.015 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.956 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.917 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.915 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.907 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.865 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.768 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.747 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.746 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.738 | |
| 4k6m | SAH | Genome polyprotein | / | 0.736 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.732 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.729 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.728 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.727 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.727 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.723 | |
| 3p97 | SAM | Genome polyprotein | 2.1.1.56 | 0.721 | |
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 0.720 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.716 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.716 | |
| 3lkz | SFG | Genome polyprotein | / | 0.716 | |
| 5jdz | SAH | Methyl transferase | / | 0.716 | |
| 3ely | SAH | Methyltransferase | / | 0.713 | |
| 3emd | SFG | Methyltransferase | / | 0.713 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.713 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.712 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.710 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.710 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.709 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.709 | |
| 1p1b | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.708 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.708 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.708 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.707 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.706 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.706 | |
| 5jjr | SAH | Genome polyprotein | / | 0.705 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.703 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.703 | |
| 4ctj | SAM | Genome polyprotein | / | 0.702 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.701 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.699 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.697 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.697 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.697 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.697 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.696 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.696 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.695 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.695 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.694 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.694 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.694 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.693 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.693 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.692 | |
| 3eld | SFG | Methyltransferase | / | 0.692 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.690 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.690 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.690 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.689 | |
| 4ctk | SAM | Genome polyprotein | / | 0.689 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.688 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.686 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.686 | |
| 5je3 | SAH | Methyl transferase | / | 0.686 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.685 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.685 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.684 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.684 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.682 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.682 | |
| 3evc | SAH | Genome polyprotein | 2.1.1.56 | 0.682 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.682 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.681 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.680 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.680 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.679 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.679 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.678 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.678 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.678 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.678 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.677 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.677 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.676 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.676 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.676 | |
| 3elu | SAM | Methyltransferase | / | 0.676 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.676 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.676 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.676 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.675 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.675 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.674 | |
| 4kvz | SAH | PtnL protein | / | 0.674 | |
| 3cbg | SAH | O-methyltransferase | / | 0.673 | |
| 4eki | 0QK | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.673 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.672 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.672 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.672 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.671 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.671 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.671 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.671 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.671 | |
| 4uck | SAM | Large structural protein | / | 0.671 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.670 | |
| 5dto | SAH | Genome polyprotein | / | 0.670 | |
| 2p3q | SAH | Genome polyprotein | / | 0.669 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.669 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.669 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.668 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.667 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.667 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.667 | |
| 3lbf | SAH | Protein-L-isoaspartate O-methyltransferase | 2.1.1.77 | 0.667 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.667 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.666 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.666 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.665 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.665 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.665 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.664 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.664 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.664 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.663 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.663 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.663 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.663 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 2xbm | SAH | Genome polyprotein | / | 0.662 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.662 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.662 | |
| 2oy0 | SAH | Genome polyprotein | / | 0.661 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.661 | |
| 3uox | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.661 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.660 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.660 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.659 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.659 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.659 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.659 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.657 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.657 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.657 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.656 | |
| 4er6 | AW2 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.655 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.655 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.655 | |
| 3c3y | SAH | O-methyltransferase | / | 0.654 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.654 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.653 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.653 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.653 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.653 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.651 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.651 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.651 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.651 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.651 | |
| 3p8z | 36A | Genome polyprotein | 2.1.1.56 | 0.651 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.651 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.651 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.650 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.650 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.650 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.650 | |
| 4gf5 | SAH | CalS11 | / | 0.650 |