4COD | pdb_00004cod

Encoded library technology as a source of hits for the discovery and lead optimization of a potent and selective class of bactericidal direct inhibitors of Mycobacterium tuberculosis InhA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.206 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4COD

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Encoded Library Technology as a Source of Hits for the Discovery and Lead Optimization of a Potent and Selective Class of Bactericidal Direct Inhibitors of Mycobacterium Tuberculosis Inha.

Encinas, L.O'Keefe, H.Neu, M.Remuinan, M.J.Patel, A.M.Guardia, A.Davie, C.P.Perez-Macias, N.Yang, H.Convery, M.A.Messer, J.A.Perez-Herran, E.Centrella, P.A.Alvarez-Gomez, D.Clark, M.A.Huss, S.O'Donovan, G.K.Ortega-Muro, F.Mcdowell, W.Castaneda, P.Arico-Muendel, C.C.Pajk, S.Rullas, J.Angulo-Barturen, I.Alvarez-Ruiz, E.Mendoza-Losana, A.Pages, L.B.Castro-Pichel, J.Evindar, G.

(2014) J Med Chem 57: 1276

  • DOI: https://doi.org/10.1021/jm401326j
  • Primary Citation Related Structures: 
    4COD

  • PubMed Abstract: 

    Tuberculosis (TB) is one of the world's oldest and deadliest diseases, killing a person every 20 s. InhA, the enoyl-ACP reductase from Mycobacterium tuberculosis, is the target of the frontline antitubercular drug isoniazid (INH). Compounds that directly target InhA and do not require activation by mycobacterial catalase peroxidase KatG are promising candidates for treating infections caused by INH resistant strains. The application of the encoded library technology (ELT) to the discovery of direct InhA inhibitors yielded compound 7 endowed with good enzymatic potency but with low antitubercular potency. This work reports the hit identification, the selected strategy for potency optimization, the structure-activity relationships of a hundred analogues synthesized, and the results of the in vivo efficacy studies performed with the lead compound 65.


  • Organizational Affiliation
    • ELT Boston, Platform Technology & Science, GlaxoSmithKline , Waltham, Massachusetts 02451, United States.

Macromolecule Content 

  • Total Structure Weight: 118.62 kDa 
  • Atom Count: 8,672 
  • Modeled Residue Count: 1,072 
  • Deposited Residue Count: 1,076 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]A [auth B],
B [auth D],
C [auth F],
D [auth H]
269Mycobacterium tuberculosisMutation(s): 0 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
F [auth B],
H [auth D],
I [auth F],
L [auth H]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
KV1

Query on KV1



Download:Ideal Coordinates CCD File
E [auth B],
G [auth D],
J [auth F],
K [auth H]
N-((3R,5S)-1-(benzofuran-3-carbonyl)-5-(ethylcarbamoyl)pyrrolidin-3-yl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide
C23 H27 N5 O4
NCHSTBMDNNMMEJ-BEFAXECRSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KV1 BindingDB:  4COD IC50: 34 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.206 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.18α = 90
b = 102.35β = 90
c = 179.36γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2014-03-19
    Changes: Refinement description
  • Version 1.3: 2014-06-11
    Changes: Refinement description
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description