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 |
|---|---|---|---|
| 4yv1 | S4M | Spermidine synthase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4yv1 | S4M | Spermidine synthase, putative | / | 1.052 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 1.009 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.979 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.974 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.955 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.865 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.780 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.779 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.754 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.723 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.722 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.699 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.694 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.688 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.687 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.686 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.686 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.685 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.684 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.683 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.683 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.680 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.678 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.678 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.677 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.676 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.675 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.672 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.671 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.670 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.670 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.669 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.669 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.669 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.669 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.668 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.668 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.666 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.666 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.665 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.664 | |
| 2v7g | NAD | Urocanate hydratase | 4.2.1.49 | 0.664 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.663 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.663 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.661 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.660 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.659 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.658 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.657 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.657 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.656 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.656 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.656 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.655 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.655 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.654 | |
| 3tos | SAH | CalS11 | / | 0.653 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.652 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.651 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.650 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.650 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.650 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.650 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.650 |