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 |
|---|---|---|---|
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 1.083 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.898 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.883 | |
| 2pa3 | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.836 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.820 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.802 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.763 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.758 | |
| 2o4c | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.757 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.755 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.752 | |
| 1psd | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.746 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.740 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.739 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.737 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.733 | |
| 2vhz | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.732 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.719 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.717 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.716 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.713 | |
| 1j5p | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.708 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.701 | |
| 2dt5 | NAD | Redox-sensing transcriptional repressor Rex | / | 0.697 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.695 | |
| 3qvt | NAI | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.694 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.692 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.691 | |
| 1o6z | NAD | Malate dehydrogenase | / | 0.688 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.684 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.683 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.682 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.679 | |
| 5dt9 | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.677 | |
| 4c4o | NAD | SADH | / | 0.676 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.676 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.676 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.675 | |
| 1sc6 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.675 | |
| 4ros | APR | Malate dehydrogenase | / | 0.674 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.673 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.673 | |
| 3abi | NAD | Uncharacterized protein | / | 0.672 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.670 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.670 | |
| 1i36 | NAP | Conserved protein | / | 0.668 | |
| 1r37 | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.668 | |
| 2dfd | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.668 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.668 | |
| 4njo | NAD | D-3-phosphoglycerate dehydrogenase, putative | / | 0.668 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.668 | |
| 1la2 | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.667 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.665 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.665 | |
| 4weq | NAP | NAD-dependent dehydrogenase | / | 0.665 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.664 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.663 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.662 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.662 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.662 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.661 | |
| 2jhf | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.660 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.658 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.656 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.655 | |
| 3keq | NAD | Redox-sensing transcriptional repressor Rex | / | 0.655 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.654 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.654 | |
| 2nad | NAD | Formate dehydrogenase | / | 0.654 | |
| 2q3e | NAI | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.654 | |
| 1bdm | NAX | Malate dehydrogenase | / | 0.653 | |
| 1ib6 | NAD | Malate dehydrogenase | / | 0.652 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.652 | |
| 4e5n | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.652 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.651 | |
| 1wze | NAD | Malate dehydrogenase | / | 0.650 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.650 |