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 |
|---|---|---|---|
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 1.151 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.991 | |
| 4e5n | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.917 | |
| 4e5m | NAP | Phosphonate dehydrogenase | 1.20.1.1 | 0.902 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.880 | |
| 2nad | NAD | Formate dehydrogenase | / | 0.752 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.751 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.749 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.747 | |
| 1gq2 | NAP | NADP-dependent malic enzyme | 1.1.1.40 | 0.737 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.735 | |
| 5bqf | NAP | Probable hydroxyacid dehydrogenase protein | / | 0.734 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.729 | |
| 3baz | NAP | Hydroxyphenylpyruvate reductase | 1.1.1.237 | 0.727 | |
| 4weq | NAP | NAD-dependent dehydrogenase | / | 0.727 | |
| 1pj3 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.726 | |
| 2dbq | NAP | Glyoxylate reductase | 1.1.1.26 | 0.725 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.722 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.722 | |
| 2dt5 | NAD | Redox-sensing transcriptional repressor Rex | / | 0.718 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.716 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.713 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.708 | |
| 1efl | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.707 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.707 | |
| 1r37 | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.706 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.702 | |
| 1gz4 | ATP | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.701 | |
| 1j5p | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.699 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.698 | |
| 1pj2 | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.694 | |
| 1u7h | NAD | Putative ornithine cyclodeaminase | / | 0.691 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.690 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.690 | |
| 4xb2 | NDP | 319aa long hypothetical homoserine dehydrogenase | / | 0.690 | |
| 5j23 | A2R | Putative 2-hydroxyacid dehydrogenase | / | 0.690 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.689 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.689 | |
| 4plp | NAD | Homospermidine synthase | 2.5.1.44 | 0.689 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.685 | |
| 4c4o | NAD | SADH | / | 0.685 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.681 | |
| 4j43 | NAD | Uncharacterized protein | / | 0.679 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.677 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.676 | |
| 4njo | NAD | D-3-phosphoglycerate dehydrogenase, putative | / | 0.676 | |
| 2vhz | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.675 | |
| 3cea | NAD | Myo-inositol 2-dehydrogenase-like (Promiscuous) | / | 0.674 | |
| 1gv0 | NAD | Malate dehydrogenase | / | 0.672 | |
| 2v7g | NAD | Urocanate hydratase | 4.2.1.49 | 0.672 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.671 | |
| 1pj4 | ATP | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.670 | |
| 3kbo | NDP | Glyoxylate/hydroxypyruvate reductase A | / | 0.670 | |
| 5dul | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.670 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.669 | |
| 1x7d | NAD | Putative ornithine cyclodeaminase | / | 0.669 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.668 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.667 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.666 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.666 | |
| 4j49 | NAI | Uncharacterized protein | / | 0.666 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.666 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.665 | |
| 3anm | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.664 | |
| 4jk3 | NAD | Uncharacterized protein | / | 0.664 | |
| 2o4c | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.663 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.663 | |
| 4j49 | NAD | Uncharacterized protein | / | 0.660 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.658 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.658 | |
| 1emd | NAD | Malate dehydrogenase | / | 0.657 | |
| 2pv7 | NAD | T-protein | 1.3.1.12 | 0.655 | |
| 3ras | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.655 | |
| 4j4b | NAI | Uncharacterized protein | / | 0.655 | |
| 3ing | NDP | Homoserine dehydrogenase related protein | / | 0.654 | |
| 3wbf | NAP | Meso-diaminopimelate D-dehydrogenase | / | 0.654 | |
| 3abi | NAD | Uncharacterized protein | / | 0.653 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.652 | |
| 2jd0 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.650 |