7E48

Crystal structure of InhA in complex with 3-nitropropanoic acid inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7E48/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-10 Released: 2021-11-24 
• Deposition Author(s): Songsiriritthigul, C., Hanwarinroj, C., Suttipanta, N., Kamsri, P., Kittakoop, P., Pungpo, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.220 
• R-Value Work: 0.185 

Literature

Inhibition of Mycobacterium tuberculosis InhA by 3-nitropropanoic acid.

Songsiriritthigul, C., Hanwarinroj, C., Pakamwong, B., Srimanote, P., Suttipanta, N., Sureram, S., Suttisintong, K., Kamsri, P., Punkvang, A., Spencer, J., Kittakoop, P., Pungpo, P.

(2022) Proteins 90: 898-904

• PubMed: 34677871 
• DOI: https://doi.org/10.1002/prot.26268
• Primary Citation of Related Structures:  
  7E48


• PubMed Abstract: 
  

  3-Nitropropanoic acid (3NP), a bioactive fungal natural product, was previously demonstrated to inhibit growth of Mycobacterium tuberculosis. Here we demonstrate that 3NP inhibits the 2-trans-enoyl-acyl carrier protein reductase (InhA) from Mycobacterium tuberculosis with an IC ₅₀ value of 71 μM, and present the crystal structure of the ternary InhA-NAD ⁺ -3NP complex. The complex contains the InhA substrate-binding loop in an ordered, open conformation with Tyr158, a catalytically important residue whose orientation defines different InhA substrate/inhibitor complex conformations, in the "out" position. 3NP occupies a hydrophobic binding site adjacent to the NAD ⁺ cofactor and close to that utilized by the diphenyl ether triclosan, but binds predominantly via electrostatic and water-mediated hydrogen-bonding interactions with the protein backbone and NAD ⁺ cofactor. The identified mode of 3NP binding provides opportunities to improve inhibitory activity toward InhA.

---

Organizational Affiliation: 

Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, Thailand.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.44 kDa 
• Atom Count: 8,594 
• Modelled Residue Count: 1,068 
• Deposited Residue Count: 1,076 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: inhA, Rv1484, MTCY277.05 EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGR1  Go to UniProtKB:  P9WGR1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
3NP	F [auth A], H [auth B], K [auth C], M [auth D]	3-NITROPROPANOIC ACID C3 H5 N O4 WBLZUCOIBUDNBV-UHFFFAOYSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.220 
• R-Value Work: 0.185 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.39	α = 90
b = 96.39	β = 90
c = 139.5	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Songsiriritthigul, C., Hanwarinroj, C., Suttipanta, N., Kamsri, P., Kittakoop, P., Pungpo, P.

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2022-02-23
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description