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 |
|---|---|---|---|
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 1.201 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 1.054 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.784 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.778 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.772 | |
| 5je2 | SAH | Methyl transferase | / | 0.770 | |
| 3tos | SAH | CalS11 | / | 0.766 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.762 | |
| 4hh4 | SAH | CcbJ | / | 0.761 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.757 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.755 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.754 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.752 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.752 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.751 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.750 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.749 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.748 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.747 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.745 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.744 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.743 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.743 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.741 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.741 | |
| 3c3y | SAH | O-methyltransferase | / | 0.740 | |
| 4gf5 | SAH | CalS11 | / | 0.739 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.737 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.736 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.735 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.735 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.734 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.733 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.733 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.733 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.732 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.730 | |
| 3cbg | SAH | O-methyltransferase | / | 0.726 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.726 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.724 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.724 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.722 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.722 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.722 | |
| 5jdz | SAH | Methyl transferase | / | 0.722 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.721 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.720 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.720 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.719 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.719 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.719 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.717 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.716 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.716 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.716 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.715 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.714 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.714 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.713 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.713 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.713 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.712 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.711 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.711 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.711 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.709 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.709 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.708 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.708 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.707 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.707 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.706 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.705 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.705 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.704 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.702 | |
| 5je3 | SAH | Methyl transferase | / | 0.702 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.701 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.701 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.698 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.697 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.696 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.695 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.695 | |
| 2zbp | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.694 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.693 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.693 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.693 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.692 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.692 | |
| 4e2x | SAH | Methyltransferase | / | 0.692 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.691 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.691 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.691 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.690 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.688 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.688 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.687 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.686 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.686 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.685 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.685 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.685 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.684 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.684 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.684 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.684 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.684 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.683 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.683 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.683 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.682 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.682 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.681 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.681 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.681 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.681 | |
| 4g56 | SAH | Protein arginine N-methyltransferase 5 | / | 0.680 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.678 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.678 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.678 | |
| 3gu3 | SAH | Methyltransferase | / | 0.677 | |
| 5epe | SAH | Uncharacterized protein | / | 0.677 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.676 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.675 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.675 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.675 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.675 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.674 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.673 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.673 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.673 | |
| 1p1b | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.670 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.669 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.669 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.668 | |
| 4gc9 | SAM | Dimethyladenosine transferase 1, mitochondrial | 2.1.1 | 0.668 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.667 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.666 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.666 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.665 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.665 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.665 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.664 | |
| 3eey | SAM | rRNA methylase | / | 0.664 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.664 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.664 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.663 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.663 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.663 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.663 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.663 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.663 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.662 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.661 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.661 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.660 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.659 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.658 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.658 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.658 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.657 | |
| 3m6v | SAM | Ribosomal RNA small subunit methyltransferase F | / | 0.657 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.657 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.657 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.657 | |
| 2cww | SAH | Uncharacterized protein | / | 0.656 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.656 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.656 | |
| 5bw4 | SAM | Uncharacterized protein | / | 0.656 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.655 | |
| 2xvm | SAH | Tellurite methyltransferase | 2.1.1.265 | 0.655 | |
| 3lst | SAH | CalO1 | / | 0.653 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.653 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.653 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.652 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.652 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.652 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.651 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.651 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.651 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.650 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.650 |