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 |
|---|---|---|---|
| 1emd | NAD | Malate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1emd | NAD | Malate dehydrogenase | / | 1.132 | |
| 1ib6 | NAD | Malate dehydrogenase | / | 0.819 | |
| 2dfd | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.748 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.745 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.738 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.723 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.717 | |
| 1r37 | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.712 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.709 | |
| 1lld | NAD | L-lactate dehydrogenase 2 | 1.1.1.27 | 0.706 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.702 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.700 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.700 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.698 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.695 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.694 | |
| 4ywj | NAD | 4-hydroxy-tetrahydrodipicolinate reductase | / | 0.690 | |
| 2eer | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.689 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.689 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.687 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.685 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.683 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.683 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.683 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.682 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.679 | |
| 2vhw | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.678 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.678 | |
| 4ros | APR | Malate dehydrogenase | / | 0.676 | |
| 4w6z | 8ID | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.676 | |
| 1m76 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.674 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.674 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.674 | |
| 4wlo | NAI | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.673 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.670 | |
| 2dt5 | NAD | Redox-sensing transcriptional repressor Rex | / | 0.669 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.669 | |
| 5kcp | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.669 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.668 | |
| 4nfs | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.668 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.665 | |
| 4j49 | NAI | Uncharacterized protein | / | 0.665 | |
| 4j4b | NAI | Uncharacterized protein | / | 0.665 | |
| 4xb2 | NDP | 319aa long hypothetical homoserine dehydrogenase | / | 0.665 | |
| 1sc6 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.664 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.662 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.662 | |
| 1bmd | NAD | Malate dehydrogenase | / | 0.660 | |
| 4e5n | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.660 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.658 | |
| 1u1i | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.658 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.658 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.658 | |
| 1x7d | NAD | Putative ornithine cyclodeaminase | / | 0.657 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.657 | |
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.657 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.655 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.655 | |
| 3nt4 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.654 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.654 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.652 | |
| 1o6z | NAD | Malate dehydrogenase | / | 0.652 | |
| 2pv7 | NAD | T-protein | 1.3.1.12 | 0.650 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.650 | |
| 5mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.650 |