5MTP

Crystal structure of M. tuberculosis InhA inhibited by PT514


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors.

Spagnuolo, L.A.Eltschkner, S.Yu, W.Daryaee, F.Davoodi, S.Knudson, S.E.Allen, E.K.Merino, J.Pschibul, A.Moree, B.Thivalapill, N.Truglio, J.J.Salafsky, J.Slayden, R.A.Kisker, C.Tonge, P.J.

(2017) J Am Chem Soc 139: 3417-3429

  • DOI: https://doi.org/10.1021/jacs.6b11148
  • Primary Citation of Related Structures:  
    5MTP, 5MTQ, 5MTR, 5UGS, 5UGT, 5UGU

  • PubMed Abstract: 

    A critical goal of lead compound selection and optimization is to maximize target engagement while minimizing off-target binding. Since target engagement is a function of both the thermodynamics and kinetics of drug-target interactions, it follows that the structures of both the ground states and transition states on the binding reaction coordinate are needed to rationally modulate the lifetime of the drug-target complex. Previously, we predicted the structure of the rate-limiting transition state that controlled the time-dependent inhibition of the enoyl-ACP reductase InhA. This led to the discovery of a triazole-containing diphenyl ether with an increased residence time on InhA due to transition-state destabilization rather than ground-state stabilization. In the present work, we evaluate the inhibition of InhA by 14 triazole-based diphenyl ethers and use a combination of enzyme kinetics and X-ray crystallography to generate a structure-kinetic relationship for time-dependent binding. We show that the triazole motif slows the rate of formation for the final drug-target complex by up to 3 orders of magnitude. In addition, we identify a novel inhibitor with a residence time on InhA of 220 min, which is 3.5-fold longer than that of the INH-NAD adduct formed by the tuberculosis drug, isoniazid. This study provides a clear example in which the lifetime of the drug-target complex is controlled by interactions in the transition state for inhibitor binding rather than the ground state of the enzyme-inhibitor complex, and demonstrates the important role that on-rates can play in drug-target residence time.


  • Organizational Affiliation

    Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]289Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: inhAMT1531
EC: 1.3.1.9
UniProt
Find proteins for P9WGR0 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P9WGR0 
Go to UniProtKB:  P9WGR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
L [auth B]
N [auth E]
P [auth G]
AA [auth H],
I [auth A],
L [auth B],
N [auth E],
P [auth G],
R [auth C],
U [auth D],
X [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
53K
Query on 53K

Download Ideal Coordinates CCD File 
BA [auth H]
J [auth A]
M [auth B]
O [auth E]
Q [auth G]
BA [auth H],
J [auth A],
M [auth B],
O [auth E],
Q [auth G],
S [auth C],
V [auth D],
Y [auth F]
2-(2-methylphenoxy)-5-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]phenol
C22 H19 N3 O2
RXXUNJCEEGMOQJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A],
T [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
CA [auth H],
W [auth D],
Z [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
53K BindingDB:  5MTP Ki: min: 229, max: 1500 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.039α = 90
b = 92.305β = 96.45
c = 181.161γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 630

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description