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 |
|---|---|---|---|
| 3kkz | SAM | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3kkz | SAM | Uncharacterized protein | / | 1.030 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.976 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.927 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.858 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.826 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.825 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.812 | |
| 4hh4 | SAH | CcbJ | / | 0.811 | |
| 3lst | SAH | CalO1 | / | 0.809 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.796 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.794 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.791 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.785 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.784 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.782 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.780 | |
| 5epe | SAH | Uncharacterized protein | / | 0.780 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.778 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.778 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.775 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.772 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.772 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.771 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.766 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.765 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.764 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.762 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.759 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.759 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.757 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.756 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.756 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.755 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.754 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.754 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.754 | |
| 4kvz | SAH | PtnL protein | / | 0.744 | |
| 4x3q | SAH | SibL | / | 0.742 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.741 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.740 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.736 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.735 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.734 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.732 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.732 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.729 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.729 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.726 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.720 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.716 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.713 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.712 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.711 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.710 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.710 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.709 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.708 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.708 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.704 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.703 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.703 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.703 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.702 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.700 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.700 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.700 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.699 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.699 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.698 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.696 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.695 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.695 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.695 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.692 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.691 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.691 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.690 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.689 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.689 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.688 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.687 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.687 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.687 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.687 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.686 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.686 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.685 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.685 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.685 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.684 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.683 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.681 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.681 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.681 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.679 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.679 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.678 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.678 | |
| 3aej | AA5 | Methionine gamma-lyase | / | 0.678 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.678 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.677 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.677 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.676 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.676 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.675 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.675 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.674 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.673 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.673 | |
| 1u4s | BIH | L-lactate dehydrogenase | 1.1.1.27 | 0.672 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.672 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.669 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.668 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.668 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.667 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.667 | |
| 2rds | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.667 | |
| 3h03 | UBP | Glutamate receptor 2 | / | 0.667 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.667 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.666 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.666 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.666 | |
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.665 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.664 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.664 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.664 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.664 | |
| 5je2 | SAH | Methyl transferase | / | 0.664 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.663 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.663 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.663 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.663 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.663 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.662 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.662 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.662 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.661 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.661 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.661 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.661 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.661 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.660 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.660 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.660 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.659 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.658 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.658 | |
| 4e2x | SAH | Methyltransferase | / | 0.658 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.658 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.657 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.657 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.657 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.656 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.656 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.656 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.656 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.656 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.655 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.654 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.653 | |
| 3u9e | COA | Lmo1369 protein | / | 0.653 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.653 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.653 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.652 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.652 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.652 | |
| 2zif | SAM | Methyltransferase | / | 0.651 | |
| 4ao4 | PLK | Beta-transaminase | / | 0.651 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.650 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.650 | |
| 1rx2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.650 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.650 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.650 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.650 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.650 |