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 |
|---|---|---|---|
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 1.117 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 1.042 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 1.011 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.979 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.936 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.841 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.839 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.826 | |
| 5je3 | SAH | Methyl transferase | / | 0.812 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.810 | |
| 5jdz | SAH | Methyl transferase | / | 0.807 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.798 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.796 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.784 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.782 | |
| 5epe | SAH | Uncharacterized protein | / | 0.780 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.774 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.773 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.773 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.765 | |
| 5je4 | SAH | Methyl transferase | / | 0.762 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.761 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.757 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.757 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.755 | |
| 4kvz | SAH | PtnL protein | / | 0.754 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.753 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.753 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.753 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.752 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.750 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.750 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.749 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.749 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.747 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.744 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.743 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.743 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.743 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.741 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.740 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.739 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.738 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.738 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.737 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.736 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.736 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.735 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.733 | |
| 4hh4 | SAH | CcbJ | / | 0.730 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.726 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.726 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.725 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.723 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.723 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.723 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.722 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.721 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.718 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.717 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.717 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.715 | |
| 3lst | SAH | CalO1 | / | 0.715 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.713 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.713 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.711 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.711 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.710 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.710 | |
| 4x3q | SAH | SibL | / | 0.710 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.709 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.707 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.706 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.706 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.706 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.704 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.704 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.704 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.703 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.703 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.702 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.701 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.701 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.700 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.700 | |
| 4e2x | SAH | Methyltransferase | / | 0.700 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.698 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.698 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.697 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.697 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.696 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.696 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.695 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.695 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.695 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.694 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.692 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.691 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.691 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.690 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.689 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.688 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.688 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.688 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.687 | |
| 2zif | SAM | Methyltransferase | / | 0.687 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.687 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.686 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.686 | |
| 5je2 | SAH | Methyl transferase | / | 0.686 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.685 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 3cbg | SAH | O-methyltransferase | / | 0.685 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.685 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.685 | |
| 3tos | SAH | CalS11 | / | 0.685 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.685 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.685 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.682 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.681 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.680 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.680 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.679 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.678 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.678 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.678 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.678 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.678 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.678 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.678 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.677 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.677 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.676 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.676 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.675 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.675 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.675 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.674 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.674 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.673 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.673 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.672 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.672 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.672 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.671 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.670 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.670 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.670 | |
| 4gf5 | SAH | CalS11 | / | 0.670 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.669 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.669 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.669 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.669 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.669 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.668 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.667 | |
| 2xe8 | ACP | Phosphoglycerate kinase 1 | 2.7.2.3 | 0.667 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.667 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.666 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.666 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.666 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.666 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.665 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.665 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.665 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.664 | |
| 3c3y | SAH | O-methyltransferase | / | 0.664 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.663 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.662 | |
| 3lby | SAH | Uncharacterized protein | / | 0.662 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.662 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.661 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.661 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.661 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.660 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.660 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.660 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.659 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.659 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.658 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.658 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.658 | |
| 2qa1 | FAD | PgaE | / | 0.657 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3bus | SAH | Demethylrebeccamycin-D-glucose O-methyltransferase | / | 0.656 | |
| 3gu3 | SAH | Methyltransferase | / | 0.656 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.655 | |
| 3emd | SFG | Methyltransferase | / | 0.655 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.655 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.654 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.653 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.653 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.653 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.652 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.652 | |
| 2zzn | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.652 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.652 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.651 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.651 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.651 |