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 |
|---|---|---|---|
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.936 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.862 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.832 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.811 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.809 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.802 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.797 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.785 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.785 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.777 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.773 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.764 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.761 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.754 | |
| 4rtp | SAM | DNA adenine methylase | 2.1.1.72 | 0.754 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.753 | |
| 4rtl | SFG | DNA adenine methylase | 2.1.1.72 | 0.749 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.747 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.747 | |
| 4gol | SA8 | DNA adenine methylase | 2.1.1.72 | 0.741 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.740 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.739 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.739 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.734 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.734 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.733 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.731 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.730 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.730 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.728 | |
| 3eey | SAM | rRNA methylase | / | 0.726 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.724 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.721 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.719 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.717 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.717 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.715 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.714 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.710 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.709 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.709 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.708 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.708 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.705 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.705 | |
| 1uay | ADN | Oxidoreductase | / | 0.702 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.702 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.702 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.702 | |
| 4rtn | SAH | DNA adenine methylase | 2.1.1.72 | 0.702 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.701 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.698 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.697 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.696 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.695 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.695 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.695 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.694 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.693 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.691 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.691 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.690 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.690 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.689 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.689 | |
| 2zif | SAM | Methyltransferase | / | 0.687 | |
| 3lby | SAH | Uncharacterized protein | / | 0.686 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.686 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.686 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.685 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.685 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.684 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.683 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.683 | |
| 4poo | SAM | Putative RNA methylase | / | 0.683 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.682 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.682 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.680 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.679 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.679 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.678 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.677 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.676 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.676 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.676 | |
| 8mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.676 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.675 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.675 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.674 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.674 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.674 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.673 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.673 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.671 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.670 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.669 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.669 | |
| 3c3y | SAH | O-methyltransferase | / | 0.669 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.668 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.666 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.666 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.666 | |
| 5jdz | SAH | Methyl transferase | / | 0.666 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.665 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.665 | |
| 3cbg | SAH | O-methyltransferase | / | 0.665 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.665 | |
| 4blv | SAM | Ribosomal RNA large subunit methyltransferase J | / | 0.665 | |
| 5je2 | SAH | Methyl transferase | / | 0.665 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.664 | |
| 4ctk | SAM | Genome polyprotein | / | 0.664 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.664 | |
| 1v59 | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.663 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.663 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.663 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.663 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.663 | |
| 4h0n | SAH | Dnmt2 | / | 0.663 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.662 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.662 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.662 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.662 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.661 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.661 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.660 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.660 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.660 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.659 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.659 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.659 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.659 | |
| 4tm3 | FAD | KtzI | / | 0.659 | |
| 5je4 | SAH | Methyl transferase | / | 0.659 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.658 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.658 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.657 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.657 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.656 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.656 | |
| 5d4v | SAH | Uncharacterized protein MJ0489 | / | 0.656 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.655 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.655 | |
| 3ely | SAH | Methyltransferase | / | 0.654 | |
| 3lkz | SFG | Genome polyprotein | / | 0.654 | |
| 3emd | SFG | Methyltransferase | / | 0.653 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.653 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.653 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.653 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.652 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.652 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.652 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.652 | |
| 2cww | SAH | Uncharacterized protein | / | 0.651 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.651 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.651 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.650 | |
| 3tos | SAH | CalS11 | / | 0.650 |