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 |
|---|---|---|---|
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 1.132 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.772 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.771 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.758 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.756 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.753 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.750 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.741 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.735 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.734 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.732 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.732 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.729 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.729 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.728 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.727 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.726 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.723 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.722 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.721 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.720 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.719 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.718 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.718 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.718 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.716 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.716 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.716 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.715 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.715 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.715 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.714 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.714 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.713 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.713 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.712 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.709 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.709 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.708 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.707 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.707 | |
| 2fkn | NAD | Urocanate hydratase | 4.2.1.49 | 0.705 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.705 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.704 | |
| 3lby | SAH | Uncharacterized protein | / | 0.704 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.703 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.703 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.703 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.703 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.702 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.700 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.699 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.698 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.697 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.697 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.697 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.696 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.696 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.696 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.696 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.695 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.695 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.695 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.695 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.694 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.694 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.694 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.693 | |
| 3cbg | SAH | O-methyltransferase | / | 0.693 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.693 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.692 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.692 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.691 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.691 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.688 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.688 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.685 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.685 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.685 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.683 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.683 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.683 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.683 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.682 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.682 | |
| 3e9y | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.681 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.681 | |
| 4uck | SAM | Large structural protein | / | 0.681 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.681 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.680 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.680 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.680 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.680 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.679 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.678 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.678 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.678 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.678 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.678 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.677 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.677 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.677 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.673 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.672 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.672 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.672 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.672 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.672 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.671 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.671 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.670 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.670 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.670 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.670 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.670 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.669 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.669 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.669 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.668 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.668 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.668 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.667 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.667 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.667 | |
| 3emd | SFG | Methyltransferase | / | 0.667 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.666 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.666 | |
| 4e2x | SAH | Methyltransferase | / | 0.666 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.666 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.666 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.665 | |
| 5je2 | SAH | Methyl transferase | / | 0.665 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.664 | |
| 1iy8 | NAD | Levodione reductase | / | 0.663 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.663 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.663 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.663 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.662 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.662 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.662 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.661 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.661 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.661 | |
| 3lst | SAH | CalO1 | / | 0.661 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.661 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.661 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.660 | |
| 4tlz | FAD | KtzI | / | 0.660 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.659 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.659 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.659 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.658 | |
| 3ely | SAH | Methyltransferase | / | 0.658 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.657 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.657 | |
| 4tm3 | FAD | KtzI | / | 0.657 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.656 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.656 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.656 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.656 | |
| 1uay | ADN | Oxidoreductase | / | 0.655 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.655 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.654 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.654 | |
| 5je4 | SAH | Methyl transferase | / | 0.654 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.653 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.653 | |
| 4ctj | SAM | Genome polyprotein | / | 0.653 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.652 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.652 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.651 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.651 | |
| 1aqi | SAH | Modification methylase TaqI | 2.1.1.72 | 0.650 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.650 |