9C1V | pdb_00009c1v

M. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CMX410

PDB DOI: https://doi.org/10.2210/pdb9C1V/pdb

Classification: TRANSFERASE/TRANSFERSE INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-29 Released: 2025-05-07
Deposition Author(s): Krieger, I.K., Tang, S., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.238 (Depositor), 0.243 (DCC)
R-Value Work:
0.194 (Depositor), 0.202 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A SuFEx-based TB clinical candidate irreversibly inhibits Pks13

Krieger, I.K., Sacchettini, J.C., McNamara, C.W.

To be published.

Macromolecule Content

Total Structure Weight: 115.45 kDa
Atom Count: 7,621
Modelled Residue Count: 936
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	A, B	512	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pks13, Rv3800c EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X8D2 Go to UniProtKB: I6X8D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6X8D2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D, E, F, G C, D, E, F, G, H, I	2		N/A	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ATW (Subject of Investigation/LOI) Query on A1ATW Download Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	N-(1-{3,5-difluoro-4-[(4-{[fluorodi(hydroxy)-lambda~4~-sulfanyl]oxy}phenoxy)methyl]phenyl}-1H-1,2,4-triazol-3-yl)methanesulfonamide C₁₆ H₁₅ F₃ N₄ O₆ S₂ LBQCKJQTXWRFFV-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	J [auth A], K [auth A], L [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	M [auth A] N [auth A] O [auth A] P [auth A] Q [auth A] M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C, D, E, F, G C, D, E, F, G, H, I	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.238 (Depositor), 0.243 (DCC)
R-Value Work: 0.194 (Depositor), 0.202 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.531	α = 90
b = 106.531	β = 90
c = 259.042	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Krieger, I.K.

Tang, S.

Sacchettini, J.C.

TB Structural Genomics Consortium (TBSGC)

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-040487
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01AI095208
Welch Foundation	United States	A-0015