Crystal structure of Mycobacterium tuberculosis ArgC in complex with 6-phenoxy-3-pyridinamine

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis

Gupta, P.Thomas, S.E.Zaidan, S.A.Pasillas, M.A.Cory-Wright, J.Sebastian-Perez, V.Burgess, A.Cattermole, E.Meghir, C.Abell, C.Coyne, A.G.Jacobs, W.R.Blundell, T.L.Tiwari, S.Mendes, V.

(2021) Comput Struct Biotechnol J 19: 3491-3506

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyl-gamma-glutamyl-phosphate reductase
A, B, C, D, E
A, B, C, D, E, F, G, H
354Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: argCRv1652MTCY06H11.17
Find proteins for P9WPZ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPZ9 
Go to UniProtKB:  P9WPZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPZ9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UKK (Subject of Investigation/LOI)
Query on UKK

Download Ideal Coordinates CCD File 
I [auth B]6-phenoxy-3-pyridinamine
C11 H10 N2 O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.34α = 90
b = 132.813β = 90.12
c = 122.819γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1158806

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description