Download MendeleyA SuFEx-based TB clinical candidate irreversibly inhibits Pks13
Krieger, I.K., Sacchettini, J.C., McNamara, C.W.To be published.
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
- 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 ?
- 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
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Polyketide synthase Pks13 | 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 AnnotationsExpand | |||||
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Oligosaccharides
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 | |
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1ATW (Subject of Investigation/LOI) Query on A1ATW | 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 |  | ||
| 1PE Query on 1PE | J [auth A], K [auth A], L [auth A] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | M [auth A] N [auth A] O [auth A] P [auth A] Q [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
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 | sucrose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.57 ?
- 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 ( ? ) | Angle ( ? ) |
|---|---|
| a = 106.531 | α = 90 |
| b = 106.531 | β = 90 |
| c = 259.042 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
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 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-07
Type: Initial release
