5OIP

InhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyrimidin-2-yl)piperidin-4-yl)urea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA.

Prati, F.Zuccotto, F.Fletcher, D.Convery, M.A.Fernandez-Menendez, R.Bates, R.Encinas, L.Zeng, J.Chung, C.W.De Dios Anton, P.Mendoza-Losana, A.Mackenzie, C.Green, S.R.Huggett, M.Barros, D.Wyatt, P.G.Ray, P.C.

(2018) ChemMedChem 13: 672-677

  • DOI: https://doi.org/10.1002/cmdc.201700774
  • Primary Citation of Related Structures:  
    5OIC, 5OIF, 5OIL, 5OIM, 5OIN, 5OIO, 5OIP, 5OIQ, 5OIR, 5OIS, 5OIT

  • PubMed Abstract: 

    Our findings reported herein provide support for the benefits of including functional group complexity (FGC) within fragments when screening against protein targets such as Mycobacterium tuberculosis InhA. We show that InhA fragment actives with FGC maintained their binding pose during elaboration. Furthermore, weak fragment hits with functional group handles also allowed for facile fragment elaboration to afford novel and potent InhA inhibitors with good ligand efficiency metrics for optimization.


  • Organizational Affiliation

    Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]269Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: inhARv1484MTCY277.05
EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
B [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
9WE (Subject of Investigation/LOI)
Query on 9WE

Download Ideal Coordinates CCD File 
C [auth A]1-(pyridin-3-ylmethyl)-3-(1-pyrimidin-2-ylpiperidin-4-yl)urea
C16 H20 N6 O
GHIMGULMAMLLAJ-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.14α = 90
b = 99.14β = 90
c = 141.52γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations