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 |
|---|---|---|---|
| 2dc1 | NAD | Probable L-aspartate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 1.125 | |
| 1j5p | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.947 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.729 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.715 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.711 | |
| 4c4o | NAD | SADH | / | 0.708 | |
| 3baz | NAP | Hydroxyphenylpyruvate reductase | 1.1.1.237 | 0.707 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.706 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.705 | |
| 1h2h | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.702 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.702 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.701 | |
| 4e5n | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.699 | |
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.698 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.695 | |
| 4e5m | NAP | Phosphonate dehydrogenase | 1.20.1.1 | 0.694 | |
| 2nad | NAD | Formate dehydrogenase | / | 0.692 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.690 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.684 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.683 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.683 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.682 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.681 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.681 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.680 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.677 | |
| 2dbq | NAP | Glyoxylate reductase | 1.1.1.26 | 0.675 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.675 | |
| 4emi | NAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.675 | |
| 6adh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.675 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.671 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.671 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.671 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.670 | |
| 5bqf | NAP | Probable hydroxyacid dehydrogenase protein | / | 0.670 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.669 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.668 | |
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.668 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.668 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.668 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.667 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.667 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.666 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.666 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.665 | |
| 4jk3 | NAD | Uncharacterized protein | / | 0.665 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.665 | |
| 4j49 | NAD | Uncharacterized protein | / | 0.664 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.662 | |
| 2o4c | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.661 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.661 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.660 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.660 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.660 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.659 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.658 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.658 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.657 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.657 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.656 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.656 | |
| 2dbz | NAP | Glyoxylate reductase | 1.1.1.26 | 0.656 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.656 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.656 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.656 | |
| 1a71 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.655 | |
| 4tm3 | FAD | KtzI | / | 0.655 | |
| 1bdm | NAX | Malate dehydrogenase | / | 0.654 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.654 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.654 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.654 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.654 | |
| 1sc6 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.653 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.653 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.652 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.652 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.652 | |
| 3nt4 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.652 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.651 | |
| 1psd | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.650 |