9C1D | pdb_00009c1d

Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9C1D

This is version 1.3 of the entry. See complete history

Literature

SuFEx-based antitubercular compound irreversibly inhibits Pks13.

Krieger, I.V.Sukheja, P.Yang, B.Tang, S.Selle, D.Woods, A.Engelhart, C.Kumar, P.Harbut, M.B.Liu, D.Tsuda, B.Qin, B.Bare, G.A.L.Li, G.Chi, V.Gambacurta, J.Hvizdos, J.Reagan, M.Jones, I.L.Massoudi, L.M.Woolhiser, L.K.Cascioferro, A.Kundrick, E.Singh, P.Reiley, W.Ioerger, T.R.Kandula, D.R.McCabe, J.W.Guo, T.Alland, D.Boshoff, H.I.Schnappinger, D.Robertson, G.T.Mdluli, K.Lee, K.J.Dong, J.Li, S.Schultz, P.G.Joseph, S.B.Love, M.S.Sharpless, K.B.Petrassi, H.M.Chatterjee, A.K.Sacchettini, J.C.McNamara, C.W.

(2025) Nature 645: 755-763

  • DOI: https://doi.org/10.1038/s41586-025-09286-3
  • Primary Citation Related Structures: 
    9C0P, 9C1C, 9C1D, 9C1V, 9C2R, 9C9O

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) remains the world's deadliest bacterial pathogen 1 . There is an urgent medical need to develop new drugs that shorten the treatment duration to combat widespread multi-drug-resistant and extensive-drug-resistant Mtb. Here, we present a preclinical covalent compound, CMX410, that contains an aryl fluorosulfate (SuFEx) 2 warhead and uniquely targets the acyltransferase domain of Pks13, an essential enzyme in cell-wall biosynthesis. CMX410 is equipotent against drug-sensitive and drug-resistant strains of Mtb and efficacious in multiple mouse models of infection. Inhibition by CMX410 is irreversible through a previously undescribed mechanism: CMX410 reacts with the catalytic serine of the AT domain of Pks13, rapidly and irreversibly disabling the active site by forming a β-lactam. CMX410 is highly selective for its target and thus demonstrates excellent pharmacological and safety profiles, including no adverse effects in a 14-day rat toxicity study up to 1,000 mg kg -1 per day. The distinctive mode of action from current drugs, high potency across all tested clinical isolates, oral bioavailability, favourable performance in drug combination testing and superior pharmacological and safety characteristics make CMX410 a promising first-in-class candidate to replace outdated cell-wall biosynthesis inhibitors, such as isoniazid and ethambutol, in tuberculosis regimens.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 164.14 kDa 
  • Atom Count: 8,056 
  • Modeled Residue Count: 948 
  • Deposited Residue Count: 1,473 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyketide synthase Pks13
A, B, C
491Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pks13Rv3800c
EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6X8D2 
Go to UniProtKB:  I6X8D2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6X8D2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE5

Query on PE5



Download:Ideal Coordinates CCD File
K [auth A]3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
P33

Query on P33



Download:Ideal Coordinates CCD File
NA [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
BA [auth A]
CB [auth B]
DA [auth A]
P [auth A]
T [auth A]
BA [auth A],
CB [auth B],
DA [auth A],
P [auth A],
T [auth A],
TA [auth B],
X [auth A],
XA [auth B],
Y [auth A],
Z [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
HB [auth C]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
HB [auth C],
I [auth A],
J [auth A],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A]
PA [auth B]
RA [auth B]
S [auth A]
SA [auth B]
D [auth A],
PA [auth B],
RA [auth B],
S [auth A],
SA [auth B],
U [auth A],
VA [auth B],
WA [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AB [auth B]
BB [auth B]
CA [auth A]
DB [auth B]
EA [auth A]
AB [auth B],
BB [auth B],
CA [auth A],
DB [auth B],
EA [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
OA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
UA [auth B],
V [auth A],
W [auth A],
YA [auth B],
ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
EB [auth B]
FA [auth A]
FB [auth B]
GA [auth A]
GB [auth B]
EB [auth B],
FA [auth A],
FB [auth B],
GA [auth A],
GB [auth B],
HA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
IA [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.183α = 90
b = 106.183β = 90
c = 259.679γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI095208
Welch FoundationUnited StatesA-0015
Bill & Melinda Gates FoundationUnited StatesINV-040487

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references
  • Version 1.2: 2025-08-13
    Changes: Database references
  • Version 1.3: 2025-10-01
    Changes: Database references