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Structure-activity relationship guides enantiomeric preference among potent inhibitors of B. anthracis dihydrofolate reductase
Analyse Structure-activity relationship guides enantiomeric preference among potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ELE
- Type
- protein
- Length
- 1,328 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- Q81R22
- Ligands
- 31I, CA, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Dihydrofolate reductase (EC 1.5.1.3) | protein | 166 | 21% helix, 32% strand | Q81R22 |
Ligands and binding sites
- 31I · (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(propan-2-yl)phthalazin-2(1H)-yl]prop-2-en -1-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, H, C, D, E, F, G
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.74 | 0.81 | 59 | CL, 31I |
| 2 | 468 | 0.71 | 0.81 | 52 | CL, 31I |
| 3 | 306 | 0.71 | 0.84 | 42 | CL, 31I |
| 4 | 354 | 0.69 | 0.82 | 44 | CL, 31I |
| 5 | 372 | 0.69 | 0.81 | 44 | CL, 31I |
Interfaces
15 interfaces between chains.
- B–F · 455 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 432 Ų buried · 5 hydrogen bonds · protein-protein
- B–H · 429 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 416 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4ELE · Structure-activity relationship guides enantiomeric preference among potent inhibitors of… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q81R22
- Elsewhere: RCSB PDB 4ELE · PDBe 4ELE · UniProt Q81R22
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