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 |
|---|---|---|---|
| 5jdz | SAH | Methyl transferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5jdz | SAH | Methyl transferase | / | 1.062 | |
| 5je3 | SAH | Methyl transferase | / | 1.056 | |
| 5je4 | SAH | Methyl transferase | / | 0.961 | |
| 5je2 | SAH | Methyl transferase | / | 0.943 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.841 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.841 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.827 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.826 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.824 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.823 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.823 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.818 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.811 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.807 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.807 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.804 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.800 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.798 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.796 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.794 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.794 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.794 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.792 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.790 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.789 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.788 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.787 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.787 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.787 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.786 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.784 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.783 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.781 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.778 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.776 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.773 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.773 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.772 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.771 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.767 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.767 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.767 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.764 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.763 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.761 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.760 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.756 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.751 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.750 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.748 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.743 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.743 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.743 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.742 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.741 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.739 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.739 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.739 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.736 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.735 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.734 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.730 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.729 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.729 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.726 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.726 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.725 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.725 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.725 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.722 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.721 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.719 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.718 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.716 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.716 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.713 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.712 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.712 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.712 | |
| 4hh4 | SAH | CcbJ | / | 0.712 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.711 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.710 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.710 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.710 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.709 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.708 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.708 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.708 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.707 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.706 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.706 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.704 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.703 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.703 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.702 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.702 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.702 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.701 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.701 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.700 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.699 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.699 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.698 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.697 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.697 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.697 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.696 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.695 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.695 | |
| 4e2x | SAH | Methyltransferase | / | 0.694 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.693 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.693 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.693 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.693 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.692 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.691 | |
| 3cbg | SAH | O-methyltransferase | / | 0.691 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.691 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.690 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.689 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.688 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.688 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.687 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.686 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.686 | |
| 1aqi | SAH | Modification methylase TaqI | 2.1.1.72 | 0.685 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.685 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.684 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.684 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.683 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.683 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.683 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.683 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.682 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.681 | |
| 3lst | SAH | CalO1 | / | 0.681 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.680 | |
| 4x3q | SAH | SibL | / | 0.680 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.679 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.679 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.679 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.678 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.678 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.678 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.678 | |
| 5epe | SAH | Uncharacterized protein | / | 0.677 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.676 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.676 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.676 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.676 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.676 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.676 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.675 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.675 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.674 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.674 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.674 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.673 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.672 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.672 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.671 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.669 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.668 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.668 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.668 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.668 | |
| 4tm3 | FAD | KtzI | / | 0.667 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.667 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.666 | |
| 3emd | SFG | Methyltransferase | / | 0.666 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.666 | |
| 4tm4 | FDA | KtzI | / | 0.664 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.663 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.663 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.663 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.663 | |
| 2dji | FAD | Pyruvate oxidase | / | 0.662 | |
| 1zx9 | FAD | Mercuric reductase | 1.16.1.1 | 0.661 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.661 | |
| 2wzb | ADP | Phosphoglycerate kinase 1 | 2.7.2.3 | 0.661 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.660 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.660 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.660 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.660 | |
| 4tm0 | FAD | KtzI | / | 0.660 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.660 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.659 | |
| 3tos | SAH | CalS11 | / | 0.659 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.659 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.659 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.658 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.657 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.657 | |
| 2zbp | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.657 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.657 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.656 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.656 | |
| 1txz | APR | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.656 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.656 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.656 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.656 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.656 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.655 | |
| 4ctk | SAM | Genome polyprotein | / | 0.655 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.654 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.654 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.654 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.654 | |
| 4poo | SAM | Putative RNA methylase | / | 0.654 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.653 | |
| 3lkz | SFG | Genome polyprotein | / | 0.653 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.653 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.653 | |
| 2zgv | ADP | Phosphoglycerate kinase 1 | 2.7.2.3 | 0.652 | |
| 3c3y | SAH | O-methyltransferase | / | 0.652 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.651 | |
| 3ely | SAH | Methyltransferase | / | 0.651 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.651 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.651 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.650 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.650 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.650 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.650 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.650 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.650 |