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 |
|---|---|---|---|
| 5epe | SAH | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5epe | SAH | Uncharacterized protein | / | 1.050 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.987 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.789 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.785 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.780 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.780 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.769 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.766 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.765 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.759 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.755 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.750 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.740 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.740 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.739 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.738 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.736 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.733 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.730 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.727 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.726 | |
| 4kvz | SAH | PtnL protein | / | 0.725 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.724 | |
| 5je2 | SAH | Methyl transferase | / | 0.723 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.721 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.720 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.720 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.719 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.719 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.719 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.718 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.718 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.716 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.716 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.712 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.712 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.708 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.708 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.708 | |
| 5je3 | SAH | Methyl transferase | / | 0.707 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.705 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.705 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.704 | |
| 5je4 | SAH | Methyl transferase | / | 0.703 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.701 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.700 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.699 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.699 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.699 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.698 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.698 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.695 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.693 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.693 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.693 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.693 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.691 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.690 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.690 | |
| 5ahk | FAD | Acetolactate synthase II, large subunit | / | 0.690 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.690 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.689 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.689 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.689 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.688 | |
| 4e2x | SAH | Methyltransferase | / | 0.688 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.688 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.687 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.687 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.687 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.686 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.685 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.685 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.684 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.684 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.684 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.684 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.682 | |
| 4x3q | SAH | SibL | / | 0.682 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.681 | |
| 4hh4 | SAH | CcbJ | / | 0.680 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.679 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.679 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.679 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.679 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.679 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.679 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.678 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.677 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.677 | |
| 5jdz | SAH | Methyl transferase | / | 0.677 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.676 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.675 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.674 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.674 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.674 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.672 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.672 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.672 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.671 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.670 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.669 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.669 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.669 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.668 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.667 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.666 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.666 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.666 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.666 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.665 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.665 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.665 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.664 | |
| 3qgz | ADN | Histidine triad nucleotide-binding protein 1 | 3 | 0.664 | |
| 4a6d | SAM | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.664 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.664 | |
| 1v5e | FAD | Pyruvate oxidase | / | 0.663 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.663 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.662 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.662 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.661 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.661 | |
| 2zif | SAM | Methyltransferase | / | 0.661 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.661 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.661 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.660 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.660 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.659 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.659 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.659 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.659 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.659 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.657 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.657 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.656 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.656 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.656 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.656 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.655 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.654 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.654 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.654 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.653 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.653 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.652 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.652 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.651 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.651 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.651 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.651 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.650 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.650 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.650 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.650 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.650 |