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 |
|---|---|---|---|
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.989 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.924 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.911 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.903 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.898 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.896 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.886 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.885 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.882 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.871 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.851 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.844 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.832 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.817 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.808 | |
| 8mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.789 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.760 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.755 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.754 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.754 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.753 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.752 | |
| 2zif | SAM | Methyltransferase | / | 0.746 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.735 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.735 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.733 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.732 | |
| 3c3y | SAH | O-methyltransferase | / | 0.731 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.731 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.730 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.730 | |
| 4poo | SAM | Putative RNA methylase | / | 0.730 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.730 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.729 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.728 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.726 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.724 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.720 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.720 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.719 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.719 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.718 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.718 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.717 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.715 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.715 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.714 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.713 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.713 | |
| 3eey | SAM | rRNA methylase | / | 0.712 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.710 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.709 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.709 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.708 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.708 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.707 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.707 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.705 | |
| 3cbg | SAH | O-methyltransferase | / | 0.705 | |
| 4kvz | SAH | PtnL protein | / | 0.704 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.704 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.703 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.703 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.703 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.703 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.702 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.702 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.701 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.700 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.700 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.699 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.699 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.698 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.698 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.698 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.698 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.698 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.697 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.697 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.697 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.695 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.695 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.695 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.694 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.693 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.693 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.693 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.693 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.692 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.691 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.691 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.691 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.689 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.688 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.688 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.687 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.687 | |
| 4ctj | SAM | Genome polyprotein | / | 0.687 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.686 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.686 | |
| 4h0n | SAH | Dnmt2 | / | 0.686 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.685 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.685 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.684 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.684 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.684 | |
| 2cww | SAH | Uncharacterized protein | / | 0.683 | |
| 2fkn | NAD | Urocanate hydratase | 4.2.1.49 | 0.683 | |
| 3lst | SAH | CalO1 | / | 0.683 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.683 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.683 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.682 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.682 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.681 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.680 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.678 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.678 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.678 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.676 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.675 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.675 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.675 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.675 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.675 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.674 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.674 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.674 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.672 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.672 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.672 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.671 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.671 | |
| 4ctk | SAM | Genome polyprotein | / | 0.671 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.671 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.671 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.670 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.670 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.670 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.670 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.670 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.669 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.669 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.668 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.668 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.668 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.668 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.667 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.667 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.667 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.666 | |
| 3eld | SFG | Methyltransferase | / | 0.666 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.666 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.665 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.665 | |
| 4rtp | SAM | DNA adenine methylase | 2.1.1.72 | 0.665 | |
| 4tlx | FDA | KtzI | / | 0.665 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.664 | |
| 3emd | SFG | Methyltransferase | / | 0.664 | |
| 3tos | SAH | CalS11 | / | 0.664 | |
| 4egu | 5GP | Putative histidine triad (HIT) protein | / | 0.664 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.664 | |
| 4tm3 | FAD | KtzI | / | 0.664 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.664 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.663 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.663 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.663 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.662 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.662 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.662 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.662 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.660 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.660 | |
| 1nhs | FAD | NADH peroxidase | 1.11.1.1 | 0.659 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.659 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.659 | |
| 4eki | 0QK | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.659 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.659 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.659 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.658 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.658 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.658 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.658 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.658 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.657 | |
| 2wa2 | SAM | Genome polyprotein | / | 0.657 | |
| 3p97 | SAM | Genome polyprotein | 2.1.1.56 | 0.657 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.657 | |
| 4tm4 | FDA | KtzI | / | 0.657 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.656 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.656 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.656 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.656 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.655 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.655 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.655 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.654 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.654 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.654 | |
| 4hh4 | SAH | CcbJ | / | 0.654 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.653 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.653 | |
| 2p41 | SAH | Genome polyprotein | / | 0.653 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.653 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.653 | |
| 3wdm | ADN | 4-phosphopantoate--beta-alanine ligase | 6.3.2.36 | 0.653 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.653 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.653 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.653 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.652 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.652 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.652 | |
| 3ely | SAH | Methyltransferase | / | 0.652 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.652 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.651 | |
| 3alj | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.651 | |
| 4gol | SA8 | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 2rgj | FAD | Flavin-containing monooxygenase | / | 0.650 | |
| 3elu | SAM | Methyltransferase | / | 0.650 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.650 |