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 |
|---|---|---|---|
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 1.088 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 1.042 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.995 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.994 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.953 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.859 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.821 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.816 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.804 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.802 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.798 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.794 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.791 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.787 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.785 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.784 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.784 | |
| 4kvz | SAH | PtnL protein | / | 0.784 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.776 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.774 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.770 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.769 | |
| 5epe | SAH | Uncharacterized protein | / | 0.766 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.765 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.762 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.758 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.757 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.754 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.749 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.747 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.747 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.746 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.745 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.742 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.741 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.739 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.738 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.736 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.736 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.735 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.732 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.731 | |
| 3lst | SAH | CalO1 | / | 0.729 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.728 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.728 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.728 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.727 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.726 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.725 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.725 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.725 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.724 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.723 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.723 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.722 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.721 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.720 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.717 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.716 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.714 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.713 | |
| 4x3q | SAH | SibL | / | 0.711 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.710 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.710 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.709 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.707 | |
| 3cbg | SAH | O-methyltransferase | / | 0.707 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.707 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.706 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.706 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.704 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.704 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.703 | |
| 4hh4 | SAH | CcbJ | / | 0.702 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.699 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.698 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.698 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.698 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.696 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.695 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.695 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.694 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.693 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.693 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.693 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.693 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.692 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.691 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.690 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.689 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.689 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.688 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.688 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.688 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.688 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.688 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.686 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.686 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.685 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.685 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.685 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.685 | |
| 3tos | SAH | CalS11 | / | 0.684 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.683 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.683 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.683 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.681 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.681 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.681 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.681 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.680 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.680 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.680 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.680 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.679 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.679 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.679 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.679 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.679 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.678 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.678 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.677 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.676 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.676 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.675 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.675 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.674 | |
| 2uxx | FAJ | Lysine-specific histone demethylase 1A | 1 | 0.674 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.674 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.672 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.671 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.671 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.671 | |
| 4gf5 | SAH | CalS11 | / | 0.671 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.671 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.671 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.670 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.670 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.670 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.670 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.669 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.668 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.668 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.668 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.668 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.667 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.667 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.666 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.666 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.665 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.665 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.665 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.665 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.664 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.663 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.663 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.663 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.663 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.662 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.662 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.661 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.661 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.660 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.660 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.659 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.659 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.658 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.658 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.658 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.657 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.657 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.656 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.656 | |
| 3bus | SAH | Demethylrebeccamycin-D-glucose O-methyltransferase | / | 0.656 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.656 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.656 | |
| 1jkf | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.655 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.655 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.655 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.655 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.654 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.653 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.653 | |
| 2zzn | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.653 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.653 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.652 | |
| 4bmz | MTA | Aminodeoxyfutalosine nucleosidase | / | 0.652 | |
| 4g56 | SAH | Protein arginine N-methyltransferase 5 | / | 0.652 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.652 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.652 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.651 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.651 | |
| 4f86 | SFG | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.651 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.650 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.650 |