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 |
|---|---|---|---|
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.986 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.958 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.936 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.924 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.903 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.901 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.891 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.889 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.888 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.875 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.864 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.861 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.832 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.817 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.811 | |
| 8mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.779 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.773 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.769 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.762 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.762 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.761 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.753 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.750 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.749 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.747 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.741 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.740 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.737 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.733 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.731 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.731 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.729 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.723 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.723 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.721 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.719 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.718 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.717 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.716 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.715 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.714 | |
| 3c3y | SAH | O-methyltransferase | / | 0.714 | |
| 3cbg | SAH | O-methyltransferase | / | 0.714 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.712 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.711 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.711 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.711 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.711 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.710 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.710 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.710 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.708 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.708 | |
| 2zif | SAM | Methyltransferase | / | 0.708 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.703 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.703 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.703 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.703 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.702 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.702 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.699 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.699 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.699 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.698 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.698 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.698 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.698 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.694 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.694 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.694 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.694 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.693 | |
| 4poo | SAM | Putative RNA methylase | / | 0.693 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.693 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.692 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.691 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.691 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.690 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.690 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.690 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.690 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.689 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.689 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.688 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.687 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.687 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.686 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.686 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.686 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.686 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.686 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.686 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.685 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.685 | |
| 4h0n | SAH | Dnmt2 | / | 0.685 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.684 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.683 | |
| 3lst | SAH | CalO1 | / | 0.683 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.683 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.683 | |
| 2cww | SAH | Uncharacterized protein | / | 0.682 | |
| 2fkn | NAD | Urocanate hydratase | 4.2.1.49 | 0.681 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.680 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.680 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.680 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.678 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.678 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.678 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.678 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.677 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.676 | |
| 4uck | SAM | Large structural protein | / | 0.676 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.675 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.675 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.674 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.674 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.674 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.674 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.674 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.674 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.674 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.674 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.674 | |
| 3eey | SAM | rRNA methylase | / | 0.672 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.671 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.671 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.670 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.670 | |
| 4ctk | SAM | Genome polyprotein | / | 0.670 | |
| 4kvz | SAH | PtnL protein | / | 0.670 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.669 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.669 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.669 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.668 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.668 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.668 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.668 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.667 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.667 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.667 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.667 | |
| 3emd | SFG | Methyltransferase | / | 0.666 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.666 | |
| 4ctj | SAM | Genome polyprotein | / | 0.666 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.664 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.663 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.663 | |
| 2ixa | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.663 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.663 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.663 | |
| 4tlx | FDA | KtzI | / | 0.663 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.663 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.662 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.662 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.662 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.661 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.661 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.661 | |
| 5epe | SAH | Uncharacterized protein | / | 0.661 | |
| 1uay | ADN | Oxidoreductase | / | 0.660 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.660 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.660 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.660 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.659 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.659 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.658 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.658 | |
| 3ntd | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.658 | |
| 3tos | SAH | CalS11 | / | 0.658 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.658 | |
| 4mo2 | FDA | UDP-galactopyranose mutase | / | 0.658 | |
| 2oy0 | SAH | Genome polyprotein | / | 0.657 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.657 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.657 | |
| 4tm4 | FDA | KtzI | / | 0.657 | |
| 3alm | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.656 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.656 | |
| 1jkf | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.655 | |
| 1v59 | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.655 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.655 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.655 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.654 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.654 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.654 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.654 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.654 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.653 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.653 | |
| 3eld | SFG | Methyltransferase | / | 0.653 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.653 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.653 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.653 | |
| 4hh4 | SAH | CcbJ | / | 0.653 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.653 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.652 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.652 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.651 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.651 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.650 | |
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 0.650 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.650 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.650 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.650 |