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 |
|---|---|---|---|
| 3e23 | SAM | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3e23 | SAM | Uncharacterized protein | / | 1.089 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.783 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.778 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.772 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.771 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.770 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.769 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.766 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.765 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.760 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.759 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.753 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.751 | |
| 4x3q | SAH | SibL | / | 0.749 | |
| 4hh4 | SAH | CcbJ | / | 0.744 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.744 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.741 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.741 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.738 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.734 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.733 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.733 | |
| 5epe | SAH | Uncharacterized protein | / | 0.726 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.723 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.721 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.720 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.719 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.716 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.715 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.714 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.714 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.713 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.713 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.712 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.711 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.711 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.711 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.709 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.709 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.708 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.708 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.707 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.704 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.703 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.703 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.703 | |
| 3lst | SAH | CalO1 | / | 0.702 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.701 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.699 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.699 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.699 | |
| 5jdz | SAH | Methyl transferase | / | 0.699 | |
| 2zif | SAM | Methyltransferase | / | 0.698 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.698 | |
| 3eey | SAM | rRNA methylase | / | 0.697 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.696 | |
| 5je2 | SAH | Methyl transferase | / | 0.696 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.694 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.693 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.692 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.691 | |
| 3o7w | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.691 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.690 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.689 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.689 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.689 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.688 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.688 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.687 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.686 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.686 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.685 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.684 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.684 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.682 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.682 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.681 | |
| 5je3 | SAH | Methyl transferase | / | 0.679 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.678 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.677 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.677 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.677 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.676 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.674 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.674 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.674 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.673 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.671 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.671 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.671 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.671 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.670 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.669 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.669 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.669 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.669 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.668 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.668 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.668 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.668 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.668 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.667 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.667 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.667 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.666 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.665 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.664 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.664 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.663 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.663 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.663 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.662 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.662 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.662 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.660 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.660 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.659 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 3alj | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.658 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.657 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.657 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.657 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.656 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.656 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.656 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.656 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.656 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.656 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.656 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.655 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.655 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.654 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.654 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.653 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.653 | |
| 4txi | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.653 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.652 | |
| 2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.652 | |
| 3tos | SAH | CalS11 | / | 0.652 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.651 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.651 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.651 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.651 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.650 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.650 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.650 |