7N8M

PptT PAP(CoA) 8978B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

In Vitro and In Vivo Inhibition of the Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT by Amidinoureas.

Ottavi, S.Scarry, S.M.Mosior, J.Ling, Y.Roberts, J.Singh, A.Zhang, D.Goullieux, L.Roubert, C.Bacque, E.Lagiakos, H.R.Vendome, J.Moraca, F.Li, K.Perkowski, A.J.Ramesh, R.Bowler, M.M.Tracy, W.Feher, V.A.Sacchettini, J.C.Gold, B.S.Nathan, C.F.Aube, J.

(2022) J Med Chem 65: 1996-2022

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01565
  • Primary Citation of Related Structures:  
    7N8E, 7N8L, 7N8M

  • PubMed Abstract: 

    A newly validated target for tuberculosis treatment is phosphopantetheinyl transferase, an essential enzyme that plays a critical role in the biosynthesis of cellular lipids and virulence factors in Mycobacterium tuberculosis . The structure-activity relationships of a recently disclosed inhibitor, amidinourea (AU) 8918 ( 1 ), were explored, focusing on the biochemical potency, determination of whole-cell on-target activity for active compounds, and profiling of selective active congeners. These studies show that the AU moiety in AU 8918 is largely optimized and that potency enhancements are obtained in analogues containing a para-substituted aromatic ring. Preliminary data reveal that while some analogues, including 1 , have demonstrated cardiotoxicity (e.g., changes in cardiomyocyte beat rate, amplitude, and peak width) and inhibit Ca v 1.2 and Na v 1.5 ion channels (although not hERG channels), inhibition of the ion channels is largely diminished for some of the para-substituted analogues, such as 5k ( p -benzamide) and 5n ( p -phenylsulfonamide).


  • Organizational Affiliation

    Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4'-phosphopantetheinyl transferase PptT
A, B
244Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pptTRv2794c
EC: 2.7.8.7
UniProt
Find proteins for O33336 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O33336 
Go to UniProtKB:  O33336
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33336
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
17I (Subject of Investigation/LOI)
Query on 17I

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B],
N [auth B]
N-(2,6-diethylphenyl)-N'-(N-methylcarbamimidoyl)urea
C13 H20 N4 O
IFRGRUBTWVGYDT-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
S [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
O [auth B]
P [auth B]
E [auth A],
F [auth A],
G [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.759α = 90
b = 63.709β = 123.334
c = 79.669γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description