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 |
|---|---|---|---|
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.954 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.754 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.746 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.745 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.740 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.737 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.737 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.731 | |
| 3p2k | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.730 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.727 | |
| 4e2x | SAH | Methyltransferase | / | 0.724 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.723 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.722 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.722 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.721 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.720 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.720 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.720 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.714 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.711 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.707 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.707 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.704 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.704 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.703 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.702 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.702 | |
| 3lst | SAH | CalO1 | / | 0.701 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.701 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.700 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.698 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.697 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.696 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.695 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.694 | |
| 5epe | SAH | Uncharacterized protein | / | 0.693 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.692 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.691 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.691 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.691 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.690 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.690 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.689 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.688 | |
| 5jdz | SAH | Methyl transferase | / | 0.686 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.685 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.683 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.683 | |
| 4gf5 | SAH | CalS11 | / | 0.682 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.682 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.681 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.680 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.679 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.679 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.678 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.678 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.678 | |
| 1vq1 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.677 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.677 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.676 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.674 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.674 | |
| 3cjq | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.674 | |
| 4g56 | SAH | Protein arginine N-methyltransferase 5 | / | 0.674 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.673 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.672 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.672 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.672 | |
| 2zw9 | SAM | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.671 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.671 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.671 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.671 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.670 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.670 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.670 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.670 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.669 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.669 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.668 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.668 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.668 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.668 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.667 | |
| 5bw4 | SAM | Uncharacterized protein | / | 0.667 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.666 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.666 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.666 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.665 | |
| 4kvz | SAH | PtnL protein | / | 0.665 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.665 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.664 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.664 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.664 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.664 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.664 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.664 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.664 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.663 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.663 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.662 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.661 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.661 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.661 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.660 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.660 | |
| 5je3 | SAH | Methyl transferase | / | 0.660 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.659 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.659 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.658 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.658 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.658 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.657 | |
| 5je2 | SAH | Methyl transferase | / | 0.656 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.655 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.655 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.655 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.654 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.654 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.654 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.653 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.653 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.653 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.652 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.652 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.652 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.651 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.651 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.651 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.651 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.650 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.650 |