MolNFT v1 · #136040 · protein
Crystal structure of M. tuberculosis inha inhibited by PT504
5UGT · Enoyl-[acyl-carrier-protein] reductase [NADH]: “Crystal structure of M. tuberculosis inha inhibited by PT504”. X-ray diffraction, 2 ligands (NAD, XTW), 15 pockets (best druggability 0.84). MolNFT v1 #136040 on GenesisL1: 3D…
- PDB
- 5UGT
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADH]
- EC
- 1.3.1.9
- UniProt
- P9WGR1
- Ligands
- NAD, XTW
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 268 | 46% helix, 16% strand | P9WGR1 |
| B | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 261 | 45% helix, 17% strand | P9WGR1 |
| G | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 264 | 44% helix, 17% strand | P9WGR1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, E, G
- XTW · 2-(2-chloranylphenoxy)-5-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]phenol · ligand · 4 copies · chains A, B, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.84 | 0.89 | 51 | NAD, XTW |
| 2 | 548 | 0.84 | 0.89 | 50 | NAD, XTW |
| 3 | 1159 | 0.83 | 0.84 | 52 | empty |
| 4 | 611 | 0.82 | 0.87 | 56 | NAD, XTW |
| 5 | 719 | 0.81 | 0.85 | 69 | NAD, XTW |
Interfaces
6 interfaces between chains.
- A–B · 1552 Ų buried · 18 hydrogen bonds · protein-protein
- E–G · 1547 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1495 Ų buried · 18 hydrogen bonds · protein-protein
- A–G · 1490 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 667 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5UGT · Crystal structure of M. tuberculosis InhA inhibited by PT504 · the same entry in another collection · chain A against A, TM-score 1.00
- P9WGR1 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH]… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P9WGR1
- Elsewhere: RCSB PDB 5UGT · PDBe 5UGT · UniProt P9WGR1
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