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 |
|---|---|---|---|
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.952 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.934 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.900 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.886 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.792 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.788 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.769 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.768 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.761 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.756 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.756 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.754 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.751 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.748 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.746 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.745 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.744 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.743 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.736 | |
| 5je2 | SAH | Methyl transferase | / | 0.735 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.734 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.733 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.729 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.728 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.726 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.723 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.723 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.717 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.716 | |
| 4hh4 | SAH | CcbJ | / | 0.716 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.715 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.715 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.709 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.704 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.703 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.703 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.701 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.701 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.699 | |
| 5jdz | SAH | Methyl transferase | / | 0.699 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.697 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.697 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.696 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.695 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.693 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.690 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.690 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.689 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.689 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.689 | |
| 5epe | SAH | Uncharacterized protein | / | 0.689 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.688 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.686 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.685 | |
| 3lst | SAH | CalO1 | / | 0.685 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.685 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.684 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.684 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.684 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.683 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.683 | |
| 5je3 | SAH | Methyl transferase | / | 0.683 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.682 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.681 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.681 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.680 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.679 | |
| 3cbg | SAH | O-methyltransferase | / | 0.677 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.677 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.675 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.675 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.675 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.674 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.674 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.674 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.674 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.673 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.671 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.671 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.670 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.670 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.670 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.669 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.669 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.669 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.667 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.665 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.665 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.665 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.664 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.664 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.663 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.663 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.663 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.662 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.662 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.662 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.662 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.661 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.661 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.661 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.661 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.660 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.660 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.659 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.659 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.659 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.658 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.657 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.657 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.657 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.657 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.656 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.656 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.656 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.656 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.654 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.654 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.653 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.653 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.653 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.653 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.653 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.652 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.652 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.652 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.651 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.651 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.651 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.650 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.650 |