Co-crystal structure of optimized analog TDI-13537 provided new insights into the potency determinants of the sulfonamide inhibitor series

Experimental Data Snapshot

  • Resolution: 1.69 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Shape-Based Virtual Screening of a Billion-Compound Library Identifies Mycobacterial Lipoamide Dehydrogenase Inhibitors.

Michino, M.Beautrait, A.Boyles, N.A.Nadupalli, A.Dementiev, A.Sun, S.Ginn, J.Baxt, L.Suto, R.Bryk, R.Jerome, S.V.Huggins, D.J.Vendome, J.

(2023) ACS Bio Med Chem Au 3: 507-515

  • DOI: https://doi.org/10.1021/acsbiomedchemau.3c00046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Lpd (lipoamide dehydrogenase) in Mycobacterium tuberculosis (Mtb) is required for virulence and is a genetically validated tuberculosis (TB) target. Numerous screens have been performed over the last decade, yet only two inhibitor series have been identified. Recent advances in large-scale virtual screening methods combined with make-on-demand compound libraries have shown the potential for finding novel hits. In this study, the Enamine REAL library consisting of ∼1.12 billion compounds was efficiently screened using the GPU Shape screen method against Mtb Lpd to find additional chemical matter that would expand on the known sulfonamide inhibitor series. We identified six new inhibitors with IC 50 in the range of 5-100 μM. While these compounds remained chemically close to the already known sulfonamide series inhibitors, some diversity was found in the cores of the hits. The two most potent hits were further validated by one-step potency optimization to submicromolar levels. The co-crystal structure of optimized analogue TDI-13537 provided new insights into the potency determinants of the series.

  • Organizational Affiliation

    Sanders Tri-Institutional Therapeutics Discovery Institute, 1230 York Avenue, Box 122, New York, New York 10065, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrolipoyl dehydrogenase
A, B
466Mycobacterium tuberculosisMutation(s): 0 
Gene Names: lpdClpdRv0462MTV038.06
Find proteins for P9WHH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHH9 
Go to UniProtKB:  P9WHH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHH9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
BA [auth B],
C [auth A]
C27 H33 N9 O15 P2
Query on U4I

Download Ideal Coordinates CCD File 
D [auth A],
Y [auth A]
C19 H21 F2 N3 O4 S
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
EA [auth B]
AA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Z [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.69 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.335α = 90
b = 97.928β = 90
c = 123.806γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release