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 |
|---|---|---|---|
| 3t4e | NAD | Quinate/shikimate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 1.183 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 1.031 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 1.012 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.931 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.896 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.881 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.811 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.766 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.753 | |
| 2vq3 | NAP | Metalloreductase STEAP3 | / | 0.725 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.717 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.712 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.712 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.707 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.704 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.703 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.699 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.696 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.696 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.692 | |
| 1do8 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.685 | |
| 1q0q | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.684 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.678 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.677 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.677 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.676 | |
| 4oaq | NDP | R-specific carbonyl reductase | / | 0.675 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.674 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.671 | |
| 3anm | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.671 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.671 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.670 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.669 | |
| 3zhb | NAP | Putative dehydrogenase | / | 0.667 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.667 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.666 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.666 | |
| 5ijz | NAP | NADP-specific glutamate dehydrogenase | 1.4.1.4 | 0.666 | |
| 1nvm | NAD | Acetaldehyde dehydrogenase | 1.2.1.10 | 0.665 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.665 | |
| 3pdu | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.665 | |
| 1h6d | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.664 | |
| 4xb2 | NDP | 319aa long hypothetical homoserine dehydrogenase | / | 0.662 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.661 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.660 | |
| 1efl | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.659 | |
| 2i9p | NAD | 3-hydroxyisobutyrate dehydrogenase, mitochondrial | 1.1.1.31 | 0.659 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.659 | |
| 1pj3 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.658 | |
| 3keo | NAD | Redox-sensing transcriptional repressor Rex | / | 0.658 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.656 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.656 | |
| 5env | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.656 | |
| 1lld | NAD | L-lactate dehydrogenase 2 | 1.1.1.27 | 0.655 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.655 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.655 | |
| 2d2i | NAP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.654 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.654 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.654 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.654 | |
| 2ixb | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.653 | |
| 3q2k | NAI | Probable oxidoreductase | / | 0.653 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.653 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.653 | |
| 3hwr | NDP | 2-dehydropantoate 2-reductase | / | 0.652 | |
| 4gae | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.652 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.652 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.651 | |
| 1u7h | NAD | Putative ornithine cyclodeaminase | / | 0.651 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.650 |