Crystal Structure of Haemophilus Influenzae Biotin Carboxylase Complexed with 7-((1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hexan-3-yl)-6-(2-chloro-6-(pyridin-3-yl)phenyl)pyrido[2,3-d]pyrimidin-2-amine

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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This is version 1.3 of the entry. See complete history


Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase.

Andrews, L.D.Kane, T.R.Dozzo, P.Haglund, C.M.Hilderbrandt, D.J.Linsell, M.S.Machajewski, T.McEnroe, G.Serio, A.W.Wlasichuk, K.B.Neau, D.B.Pakhomova, S.Waldrop, G.L.Sharp, M.Pogliano, J.Cirz, R.T.Cohen, F.

(2019) J Med Chem 62: 7489-7505

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00625
  • Primary Citation of Related Structures:  
    6OI8, 6OI9

  • PubMed Abstract: 

    A major challenge for new antibiotic discovery is predicting the physicochemical properties that enable small molecules to permeate Gram-negative bacterial membranes. We have applied physicochemical lessons from previous work to redesign and improve the antibacterial potency of pyridopyrimidine inhibitors of biotin carboxylase (BC) by up to 64-fold and 16-fold against Escherichia coli and Pseudomonas aeruginosa , respectively. Antibacterial and enzyme potency assessments in the presence of an outer membrane-permeabilizing agent or in efflux-compromised strains indicate that penetration and efflux properties of many redesigned BC inhibitors could be improved to various extents. Spontaneous resistance to the improved pyridopyrimidine inhibitors in P. aeruginosa occurs at very low frequencies between 10 -8 and 10 -9 . However, resistant isolates had alarmingly high minimum inhibitory concentration shifts (16- to >128-fold) compared to the parent strain. Whole-genome sequencing of resistant isolates revealed that either BC target mutations or efflux pump overexpression can lead to the development of high-level resistance.

  • Organizational Affiliation

    Linnaeus Bioscience Inc. , 3210 Merryfield Row , San Diego , California 92121 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biotin carboxylase468Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: accCHI_0972
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P43873 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P43873 
Go to UniProtKB:  P43873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43873
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MQV

Download Ideal Coordinates CCD File 
C [auth A]7-[(1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hexan-3-yl]-6-[2-chloro-6-(pyridin-3-yl)phenyl]pyrido[2,3-d]pyrimidin-2-amine
C23 H20 Cl N7
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.321α = 90
b = 86.321β = 90
c = 102.75γ = 120
Software Package:
Software NamePurpose
xia2data reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI113572

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description