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 |
|---|---|---|---|
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 1.065 | |
| 1la2 | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.827 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.784 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.738 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.733 | |
| 3qvt | NAI | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.728 | |
| 3ec7 | NAD | Inositol 2-dehydrogenase | / | 0.714 | |
| 1j5p | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.711 | |
| 1xcb | NAD | Redox-sensing transcriptional repressor Rex | / | 0.699 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.697 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.690 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.690 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.690 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.689 | |
| 1u1i | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.688 | |
| 4tm3 | FAD | KtzI | / | 0.686 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.684 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.680 | |
| 4c4o | NAD | SADH | / | 0.679 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.678 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.676 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.676 | |
| 4j49 | NAD | Uncharacterized protein | / | 0.676 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.675 | |
| 1h2h | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.675 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.675 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.672 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.672 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.672 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.671 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.671 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.671 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.671 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.669 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.669 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.668 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.668 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.667 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.667 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.667 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.667 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.666 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.666 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.665 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.665 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.663 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.663 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.663 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.662 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.660 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.660 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.659 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.659 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.659 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.658 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.658 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.657 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.656 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.656 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.655 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.655 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.654 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.654 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.653 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.652 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.652 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.651 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.650 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.650 |