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 |
|---|---|---|---|
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 1.033 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.915 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.895 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.861 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.826 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.797 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.787 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.775 | |
| 3emd | SFG | Methyltransferase | / | 0.762 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.753 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.752 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.750 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.741 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.739 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.737 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.735 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.731 | |
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 0.729 | |
| 3evc | SAH | Genome polyprotein | 2.1.1.56 | 0.729 | |
| 3p97 | SAM | Genome polyprotein | 2.1.1.56 | 0.727 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.727 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.726 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.726 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.720 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.720 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.717 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.716 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.714 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.713 | |
| 3vyw | SAM | Uncharacterized protein | / | 0.712 | |
| 4ctj | SAM | Genome polyprotein | / | 0.707 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.707 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.706 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.706 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.706 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.705 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.703 | |
| 2wa2 | SAM | Genome polyprotein | / | 0.703 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.702 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.701 | |
| 3lkz | SFG | Genome polyprotein | / | 0.698 | |
| 5jdz | SAH | Methyl transferase | / | 0.697 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.696 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.696 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.696 | |
| 4k6m | SAH | Genome polyprotein | / | 0.695 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.694 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.693 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.693 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.693 | |
| 4gek | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.693 | |
| 5je2 | SAH | Methyl transferase | / | 0.691 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.690 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.689 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.688 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.687 | |
| 3ely | SAH | Methyltransferase | / | 0.687 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.687 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.686 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.686 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.686 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.685 | |
| 4ctk | SAM | Genome polyprotein | / | 0.685 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.684 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.684 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.684 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.683 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.683 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.682 | |
| 3c3y | SAH | O-methyltransferase | / | 0.682 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.682 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.681 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.681 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.680 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.680 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.680 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.680 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.680 | |
| 5jjr | SAH | Genome polyprotein | / | 0.680 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.678 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.678 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.677 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.676 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.676 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.676 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.676 | |
| 5je3 | SAH | Methyl transferase | / | 0.676 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.675 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.675 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.675 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.674 | |
| 3lbf | SAH | Protein-L-isoaspartate O-methyltransferase | 2.1.1.77 | 0.674 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.674 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.674 | |
| 4poo | SAM | Putative RNA methylase | / | 0.674 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.674 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.673 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.673 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.673 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.673 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.672 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.671 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.671 | |
| 3hvi | 619 | Catechol O-methyltransferase | 2.1.1.6 | 0.671 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.671 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.670 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.670 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.670 | |
| 1p1b | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.669 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.669 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.669 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.667 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.667 | |
| 4e2x | SAH | Methyltransferase | / | 0.667 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.666 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.666 | |
| 3eld | SFG | Methyltransferase | / | 0.666 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.665 | |
| 3cbg | SAH | O-methyltransferase | / | 0.665 | |
| 4hh4 | SAH | CcbJ | / | 0.665 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.664 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.664 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.664 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.664 | |
| 4htf | SAM | tRNA 5-carboxymethoxyuridine methyltransferase | / | 0.664 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.663 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.663 | |
| 4uck | SAM | Large structural protein | / | 0.663 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.662 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.662 | |
| 3eey | SAM | rRNA methylase | / | 0.662 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.662 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.662 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.662 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.661 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.661 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.661 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.661 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.661 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.661 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.660 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.660 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.660 | |
| 5ahk | FAD | Acetolactate synthase II, large subunit | / | 0.660 | |
| 5dto | SAH | Genome polyprotein | / | 0.660 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.659 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.659 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.658 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.657 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.657 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.656 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.656 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.656 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.656 | |
| 2qa1 | FAD | PgaE | / | 0.655 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.655 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.655 | |
| 4n48 | SAM | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 | 2.1.1.57 | 0.655 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.654 | |
| 2p3q | SAH | Genome polyprotein | / | 0.653 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.653 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.653 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.653 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 1txz | APR | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.652 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.652 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.652 | |
| 4x3q | SAH | SibL | / | 0.652 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.651 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.651 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.651 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.650 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.650 |