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 |
|---|---|---|---|
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.870 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.833 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.804 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.791 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.787 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.785 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.764 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.754 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.754 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.742 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.742 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.737 | |
| 2zif | SAM | Methyltransferase | / | 0.733 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.733 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.727 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.727 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.724 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.723 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.721 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.720 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.720 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.719 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.718 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.717 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.717 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.717 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.716 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.716 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.715 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.713 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.713 | |
| 4gol | SA8 | DNA adenine methylase | 2.1.1.72 | 0.713 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.712 | |
| 1uay | ADN | Oxidoreductase | / | 0.711 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.710 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.710 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.709 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.708 | |
| 4rtn | SAH | DNA adenine methylase | 2.1.1.72 | 0.707 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.705 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.704 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.704 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.702 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.702 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.701 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.701 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.701 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.697 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.696 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.696 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.696 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.694 | |
| 4rtp | SAM | DNA adenine methylase | 2.1.1.72 | 0.694 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.693 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.693 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.693 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.692 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.692 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.692 | |
| 3c3y | SAH | O-methyltransferase | / | 0.691 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.690 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.690 | |
| 4rtl | SFG | DNA adenine methylase | 2.1.1.72 | 0.690 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.690 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.688 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.688 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.688 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.687 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.687 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.686 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.686 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.685 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.683 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.683 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.683 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.681 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.681 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.680 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.679 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.679 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.679 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.678 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.678 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.678 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.678 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.678 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.677 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.676 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.676 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.675 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.674 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.674 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.674 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.670 | |
| 5je2 | SAH | Methyl transferase | / | 0.670 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.668 | |
| 4kvz | SAH | PtnL protein | / | 0.668 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.667 | |
| 3eey | SAM | rRNA methylase | / | 0.667 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.667 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.666 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.666 | |
| 4poo | SAM | Putative RNA methylase | / | 0.666 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.665 | |
| 3lby | SAH | Uncharacterized protein | / | 0.665 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.664 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.663 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.663 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.662 | |
| 4tlz | FAD | KtzI | / | 0.662 | |
| 2cww | SAH | Uncharacterized protein | / | 0.661 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.661 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.661 | |
| 1v59 | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.660 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.660 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.660 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.659 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.659 | |
| 5epe | SAH | Uncharacterized protein | / | 0.659 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.657 | |
| 4hh4 | SAH | CcbJ | / | 0.657 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.656 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.656 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.656 | |
| 5jjr | SAH | Genome polyprotein | / | 0.656 | |
| 3bus | SAH | Demethylrebeccamycin-D-glucose O-methyltransferase | / | 0.655 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.655 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.654 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.654 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.653 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.653 | |
| 4d79 | ATP | tRNA threonylcarbamoyladenosine dehydratase | 6.1 | 0.653 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.652 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.652 | |
| 4tlx | FDA | KtzI | / | 0.651 | |
| 8mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.650 |