9DRK | pdb_00009drk

Crystal structure of Mycobacterium tuberculosis biotin protein ligase in complex with Bio-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.262 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.193 (Depositor) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Metabolically Stable Adenylation Inhibitors of Biotin Protein Ligase as Antibacterial Agents.

Liu, Q.Engelhart, C.A.Wallach, J.B.Tiwari, D.Ge, P.Manna, A.Panda, S.McCue, W.M.Wong, T.Y.Sharma, S.Jayasinghe, Y.P.Fuller, J.Ronning, D.R.Bockman, M.R.Cheung, A.Dartois, V.Zimmerman, M.D.Schnappinger, D.Aldrich, C.C.

(2025) J Med Chem 68: 3065-3087

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02299
  • Primary Citation Related Structures: 
    9DRK, 9DRN

  • PubMed Abstract: 

    The antibacterial agent Bio-AMS is metabolized in vivo through hydrolysis of the central acyl-sulfamide linker leading to high clearance and release of a moderately cytotoxic metabolite M1 . Herein, we disclose analogues designed to prevent the metabolism of the central acyl-sulfamide moiety through steric hindrance or attenuation of the acyl-sulfamide electrophilicity. Bio-9 was identified as a metabolically stable analogue with a single-digit nanomolar dissociation constant for biotin protein ligase (BPL) and minimum inhibitory concentrations (MICs) against Mycobacterium tuberculosis and Staphylococcus aureus ranging from 0.2 to 20 μM. The antibacterial activity of Bio-9 was dependent on BPL expression level and was more than 70-fold better against a strain underexpressing BPL and, conversely, more than 5-fold less effective against a strain overexpressing BPL. Pharmacokinetic and metabolic studies demonstrated that Bio-9 was metabolically stable in vivo, showing negligible hydrolysis that translated to substantially reduced clearance and concomitantly boosted drug exposure and half-life compared to Bio-AMS.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States.

Macromolecule Content 

  • Total Structure Weight: 57.11 kDa 
  • Atom Count: 3,974 
  • Modeled Residue Count: 522 
  • Deposited Residue Count: 530 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Biotin--[acetyl-CoA-carboxylase] ligase
A, B
265Mycobacterium tuberculosisMutation(s): 0 
Gene Names: birARv3279c
EC: 6.3.4.15
UniProt
Find proteins for I6YFP0 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6YFP0 
Go to UniProtKB:  I6YFP0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6YFP0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BGE
(Subject of Investigation/LOI)

Query on A1BGE



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
5'-deoxy-5'-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}sulfamamido)adenosine
C20 H31 N9 O6 S2
XESGTLMEDWYNFU-SQGSUPJISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.262 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.193 (Depositor) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.651α = 90
b = 68.705β = 90
c = 115.134γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata 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 StatesAI143784

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release