7JT5

Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibition of Mycobacterium tuberculosis Dethiobiotin Synthase ( Mt DTBS): Toward Next-Generation Antituberculosis Agents.

Schumann, N.C.Lee, K.J.Thompson, A.P.Salaemae, W.Pederick, J.L.Avery, T.Gaiser, B.I.Hodgkinson-Bean, J.Booker, G.W.Polyak, S.W.Bruning, J.B.Wegener, K.L.Abell, A.D.

(2021) ACS Chem Biol 16: 2339-2347

  • DOI: https://doi.org/10.1021/acschembio.1c00491
  • Primary Citation of Related Structures:  
    7JT5, 7JT6, 7L1J

  • PubMed Abstract: 

    Mycobacterium tuberculosis dethiobiotin synthase ( Mt DTBS) is a crucial enzyme involved in the biosynthesis of biotin in the causative agent of tuberculosis, M. tuberculosis . Here, we report a binder of Mt DTBS, cyclopentylacetic acid 2 ( K D = 3.4 ± 0.4 mM), identified via in silico screening. X-ray crystallography showed that 2 binds in the 7,8-diaminopelargonic acid (DAPA) pocket of Mt DTBS. Appending an acidic group to the para-position of the aromatic ring of the scaffold revealed compounds 4c and 4d as more potent binders, with K D = 19 ± 5 and 17 ± 1 μM, respectively. Further optimization identified tetrazole 7a as a particularly potent binder ( K D = 57 ± 5 nM) and inhibitor ( K i = 5 ± 1 μM) of Mt DTBS. Our findings highlight the first reported inhibitors of Mt DTBS and serve as a platform for the further development of potent inhibitors and novel therapeutics for the treatment of tuberculosis.


  • Organizational Affiliation

    Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent dethiobiotin synthetase BioD
A, B, C, D
233Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: bioDRv1570MTCY336.33c
EC: 6.3.3.3
UniProt
Find proteins for P9WPQ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPQ5 
Go to UniProtKB:  P9WPQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPQ5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VJS (Subject of Investigation/LOI)
Query on VJS

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C],
U [auth D]
{(1R,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}propanedioic acid
C17 H18 O7
HXTDFADOGPNOAK-VXGBXAGGSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth B]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
S [auth C],
V [auth D],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.648α = 90
b = 105.023β = 90
c = 152.719γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references
  • Version 1.2: 2021-12-01
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description