7DB8

Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex with compound PF-3845


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis .

Wang, H.Xu, M.Engelhart, C.A.Zhang, X.Yan, B.Pan, M.Xu, Y.Fan, S.Liu, R.Xu, L.Hua, L.Schnappinger, D.Chen, S.

(2021) J Biol Chem 

  • DOI: https://doi.org/10.1074/jbc.RA120.016477
  • Primary Citation of Related Structures:  
    7DAW, 7DB7, 7DB8

  • PubMed Abstract: 

    Mycobacteria tuberculosis (Mtb) remains the deadliest pathogenic bacteria worldwide. The search for new antibiotics to treat drug-sensitive as well as drug-resistant tuberculosis has become a priority. The essential enzyme phenylalanyl-tRNA synthetase (PheRS) is an antibacterial drug target because of the large differences between bacterial and human PheRS counterparts. In a high-throughput screening of 2148 bioactive compounds, PF-3845, which is a known inhibitor of human fatty acid amide hydrolase (FAAH), was identified inhibiting Mtb PheRS at K i ~0.73 ± 0.06 µM. The inhibition mechanism was studied with enzyme kinetics, protein structural modelling and crystallography, in comparison to a PheRS inhibitor of the noted phenyl-thiazolylurea-sulfonamide class. The 2.3-Å crystal structure of Mtb PheRS in complex with PF-3845 revealed its novel binding mode, in which a trifluoromethyl-pyridinylphenyl group occupies the Phe pocket while a piperidine-piperazine urea group binds into the ATP pocket through an interaction network enforced by a sulfate ion. It represents the first non-nucleoside bi-substrate competitive inhibitor of bacterial PheRS. PF-3845 inhibits the in vitro growth of Mtb H37Rv at ~24 µM, and the potency of PF-3845 increased against Mtb pheS-FDAS, suggesting on target activity in mycobacterial whole cells.  PF-3845 does not inhibit human cytoplasmic or mitochondrial PheRS in biochemical assay, which can be explained from the crystal structures. Further medicinal chemistry efforts focused on the piperidine-piperazine urea moiety may result in the identification of a selective antibacterial lead compound.


  • Organizational Affiliation

    Global Health Drug Discovery Institute, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase alpha subunit341Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pheSRv1649MTCY06H11.14
EC: 6.1.1.20
UniProt
Find proteins for P9WFU3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFU3 
Go to UniProtKB:  P9WFU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFU3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase beta subunit845Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pheTRv1650MTCY06H11.15
EC: 6.1.1.20
UniProt
Find proteins for P9WFU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFU1 
Go to UniProtKB:  P9WFU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFU1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H2R (Subject of Investigation/LOI)
Query on H2R

Download Ideal Coordinates CCD File 
F [auth A]N-pyridin-3-yl-4-[[3-[5-(trifluoromethyl)pyridin-2-yl]oxyphenyl]methyl]piperidine-1-carboxamide
C24 H23 F3 N4 O2
NBOJHRYUGLRASX-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 278.005α = 90
b = 297.814β = 90
c = 65.901γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description