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 |
|---|---|---|---|
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.969 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.916 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.904 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.901 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.888 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.886 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.872 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.871 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.861 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.852 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.844 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.832 | |
| 8mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.786 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.773 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.767 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.763 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.752 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.747 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.747 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.740 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.739 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.737 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.736 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.736 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.736 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.732 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.732 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.728 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.727 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.727 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.726 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.725 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.724 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.723 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.722 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.720 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.719 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.719 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.718 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.717 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.717 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.717 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.716 | |
| 4poo | SAM | Putative RNA methylase | / | 0.716 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.715 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.714 | |
| 2zif | SAM | Methyltransferase | / | 0.713 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.712 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.708 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.708 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.708 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.708 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.706 | |
| 3eey | SAM | rRNA methylase | / | 0.705 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.704 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.703 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.703 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.703 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.703 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.701 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.700 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.700 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.700 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.700 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.700 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.700 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.699 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.699 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.698 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.698 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.696 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.695 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.695 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.695 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.694 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.694 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.693 | |
| 4mo2 | FDA | UDP-galactopyranose mutase | / | 0.692 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.692 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.691 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.691 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.690 | |
| 3lby | SAH | Uncharacterized protein | / | 0.690 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.689 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.689 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.688 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.687 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.687 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.687 | |
| 4ctj | SAM | Genome polyprotein | / | 0.686 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.686 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.686 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.685 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.685 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.685 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.685 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.684 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.683 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.683 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.683 | |
| 4tlz | FAD | KtzI | / | 0.683 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.682 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.682 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.682 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.681 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.681 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.681 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.681 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.681 | |
| 4tlx | FDA | KtzI | / | 0.681 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.681 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.680 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.680 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.680 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.680 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.680 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.680 | |
| 4tm3 | FAD | KtzI | / | 0.680 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.679 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.679 | |
| 4tm1 | FDA | KtzI | / | 0.679 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.678 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.678 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.678 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.678 | |
| 4tm4 | FDA | KtzI | / | 0.678 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.678 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.677 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.677 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.677 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.676 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.676 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.676 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.676 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.675 | |
| 1uay | ADN | Oxidoreductase | / | 0.675 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.675 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.675 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.675 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.675 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.674 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.674 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.674 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.673 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.673 | |
| 4h0n | SAH | Dnmt2 | / | 0.673 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.673 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.672 | |
| 3c3y | SAH | O-methyltransferase | / | 0.672 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.672 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.672 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.672 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.672 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.671 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.671 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.671 | |
| 3tos | SAH | CalS11 | / | 0.671 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.671 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.671 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.670 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.670 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.670 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.669 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.669 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.669 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.669 | |
| 4ctk | SAM | Genome polyprotein | / | 0.669 | |
| 4egu | 5GP | Putative histidine triad (HIT) protein | / | 0.669 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.669 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.668 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.668 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.668 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.667 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.667 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.667 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.667 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.666 | |
| 4kvz | SAH | PtnL protein | / | 0.666 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.666 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.665 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.665 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.665 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.665 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.665 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.664 | |
| 3lhd | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.664 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.663 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.663 | |
| 3cbg | SAH | O-methyltransferase | / | 0.662 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.662 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.662 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.662 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.662 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.661 | |
| 4eqr | FAD | Coenzyme A disulfide reductase | / | 0.661 | |
| 1nhs | FAD | NADH peroxidase | 1.11.1.1 | 0.660 | |
| 2eq8 | FAD | Dihydrolipoyl dehydrogenase | / | 0.660 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.660 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.660 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.660 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.660 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.659 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.659 | |
| 4tm0 | FAD | KtzI | / | 0.659 | |
| 3ntd | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.658 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.657 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.657 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.656 | |
| 1v59 | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.656 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.656 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.656 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.656 | |
| 1npx | FAD | NADH peroxidase | 1.11.1.1 | 0.655 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.655 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.655 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.655 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.655 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.655 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.654 | |
| 2cdu | ADP | NADH oxidase | / | 0.654 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.654 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.654 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.654 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.653 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.653 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.653 | |
| 3eld | SFG | Methyltransferase | / | 0.653 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.653 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.652 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.652 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.652 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.652 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.651 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.651 | |
| 4hh4 | SAH | CcbJ | / | 0.651 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.651 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.650 | |
| 5il1 | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.650 |