MolNFT v1 · #162462 · protein
Crystal structure of inha in complex with ap-124 inhibitor
6R9W · Enoyl-[acyl-carrier-protein] reductase [NADH]: “Crystal structure of inha in complex with ap-124 inhibitor”. X-ray diffraction, 2 ligands (NAD, JVZ), 19 pockets (best druggability 0.81). MolNFT v1 #162462 on GenesisL1: 3D structure…
- PDB
- 6R9W
- Type
- protein
- Length
- 1,571 residues
- Chains
- 6
- 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, JVZ
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 267 | 46% helix, 16% strand | P9WGR1 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 263 | 46% helix, 16% strand | P9WGR1 |
| F | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 240 | 43% helix, 18% strand | P9WGR1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- JVZ · (2~{S})-1-(benzimidazol-1-yl)-3-(2,3-dihydro-1~{H}-inden-5-yloxy)propan-2-ol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.81 | 0.87 | 53 | NAD |
| 2 | 516 | 0.81 | 0.87 | 53 | NAD |
| 3 | 833 | 0.79 | 0.82 | 62 | JVZ, NAD |
| 4 | 759 | 0.79 | 0.82 | 58 | NAD |
| 5 | 1023 | 0.78 | 0.80 | 83 | NAD |
Interfaces
7 interfaces between chains.
- C–D · 1561 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1561 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1438 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 742 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 187 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6R9W · Crystal structure of InhA in complex with AP-124 inhibitor · the same entry in another collection · chain F against F, 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 F against A, TM-score 0.99
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 6R9W · PDBe 6R9W · UniProt P9WGR1
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