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 |
|---|---|---|---|
| 4hh4 | SAH | CcbJ |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4hh4 | SAH | CcbJ | / | 1.163 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.907 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.863 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.858 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.845 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.844 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.841 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.831 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.831 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.816 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.811 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.810 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.806 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.794 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.788 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.788 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.787 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.784 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.781 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.778 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.776 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.776 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.775 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.774 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.770 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.767 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.764 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.761 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.759 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.756 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.755 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.753 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.752 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.752 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.752 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.752 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.746 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.746 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.745 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.745 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.744 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.744 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.739 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.734 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.734 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.733 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.731 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.730 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.730 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.730 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.730 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.729 | |
| 5je2 | SAH | Methyl transferase | / | 0.729 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.728 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.728 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.726 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.725 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.725 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.724 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.724 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.723 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.723 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.721 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.720 | |
| 4kvz | SAH | PtnL protein | / | 0.720 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.719 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.718 | |
| 3lst | SAH | CalO1 | / | 0.717 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.717 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.716 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.715 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.714 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.713 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.713 | |
| 5jdz | SAH | Methyl transferase | / | 0.712 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.708 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.708 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.708 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.707 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.706 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.705 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.705 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.705 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.704 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.702 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.702 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.701 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.701 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.701 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.700 | |
| 4e2x | SAH | Methyltransferase | / | 0.700 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.700 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.700 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.699 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.699 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.697 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.696 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.696 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.695 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.694 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.694 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.693 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.693 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.693 | |
| 5je3 | SAH | Methyl transferase | / | 0.690 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.688 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.688 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.688 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.688 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.688 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.687 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.686 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.685 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.684 | |
| 3c3y | SAH | O-methyltransferase | / | 0.683 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.683 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.683 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.681 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.681 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.681 | |
| 3ua3 | SAH | Protein arginine N-methyltransferase 5 | / | 0.681 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.681 | |
| 5epe | SAH | Uncharacterized protein | / | 0.680 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.679 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.679 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.678 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.678 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.678 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.677 | |
| 1cq6 | PY4 | Aspartate aminotransferase | 2.6.1.1 | 0.677 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.677 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.677 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.677 | |
| 4x3q | SAH | SibL | / | 0.677 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.676 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.676 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.676 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.676 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.675 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.674 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.674 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.674 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.674 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.674 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.673 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.673 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.673 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.673 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.673 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.672 | |
| 8atc | PAL | Aspartate carbamoyltransferase catalytic subunit | 2.1.3.2 | 0.672 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.671 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.671 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.671 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.671 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.671 | |
| 2v7g | NAD | Urocanate hydratase | 4.2.1.49 | 0.670 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.670 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.670 | |
| 3okx | SAM | S-adenosyl-L-methionine-binding protein RPA0152 | / | 0.668 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.668 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.667 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.667 | |
| 4poo | SAM | Putative RNA methylase | / | 0.667 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.666 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.665 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.665 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.665 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.664 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.664 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.663 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.662 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.662 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.661 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.661 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.661 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.660 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.660 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.660 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.659 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.658 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.657 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.657 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.657 | |
| 4w5k | PLP | Aspartate aminotransferase, mitochondrial | / | 0.657 | |
| 1uay | ADN | Oxidoreductase | / | 0.655 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.655 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.655 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.654 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.654 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.654 | |
| 1u5a | BIK | L-lactate dehydrogenase | 1.1.1.27 | 0.653 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.653 | |
| 3rt8 | CWD | Glutamate receptor 3 | / | 0.653 | |
| 3s2v | 3HU | Glutamate receptor ionotropic, kainate 1 | / | 0.653 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.653 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.653 | |
| 3gu3 | SAH | Methyltransferase | / | 0.652 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.651 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.651 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.651 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.651 | |
| 3e9y | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.651 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.651 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.650 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.650 | |
| 4ce0 | SAH | Probable O-methyltransferase | / | 0.650 |