9MD8 | pdb_00009md8

Hip1 complex with inhibitor #2 (Hip1-2) via Ser228

• PDB DOI: https://doi.org/10.2210/pdb9MD8/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-12-17 
• Deposition Author(s): Yim, M.K., Schumann, N.C., Goldfarb, N.E., Johnson, S.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Discovery of highly potent alpha-keto ester-based peptidomimetic inhibitors of the Hip1 protease for the treatment of Mycobacterium tuberculosis.

Schumann, N., Shamma, F., Brooks, C.L., Johnson, S.J., Yim, M.K., Olsen, K.J., Pena, K., Karakousis, P.C., Abell, A., Goldfarb, N.E.

(2025) Eur J Med Chem Rep 15

• PubMed: 41929655 
• DOI: https://doi.org/10.1016/j.ejmcr.2025.100311
• Primary Citation Related Structures: 
  9MD7, 9MD8


• PubMed Abstract: 
  

  Mycobacterium tuberculosis (Mtb), the bacterium responsible for tuberculosis, is the leading cause of death due to a single infectious agent. Given the alarming increase in drug-resistant cases, therapeutic agents targeting novel Mtb drug targets are urgently needed. Hip1, a serine protease required for Mtb survival in macrophages and tolerance to various antibiotics, has been identified as an attractive therapeutic target. In the current study, we describe the design and synthesis of highly potent (pM range K _i ) peptidomimetic α-keto ester inhibitors of Hip1. We also report the first two X-ray cocrystal structures of Hip1 bound to these compounds and describe the binding interactions in the active site of recombinant Hip1. Finally, we show that these compounds effectively reduce the intracellular bacillary burden in a macrophage model of Mtb infection.

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Organizational Affiliation: 
• Department of Chemistry, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia.
Department of Medicine, TB Research Advancement Center, 1550 Orleans St, Baltimore, MD, 21287, USA.
Department of Chemistry and Biochemistry, California State University Fresno, 2555 E. San Ramon Ave, Fresno, CA, 93740, USA.
Department of Chemistry & Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT, 84322-0300, USA.
Department of Biochemistry, Utah Valley University, 800 W. University Parkway, Orem, UT, 84058, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.84 kDa 
• Atom Count: 3,837 
• Modeled Residue Count: 473 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	486	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: tap, ERS007688_01841 EC: 3.4 (PDB Primary Data), 3.4.14 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for P9WHR3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHR3  Go to UniProtKB:  P9WHR3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BK3	B [auth A]	N-carboxy-L-phenylalanyl-N-{(2S,3R)-3-hydroxy-4-methoxy-4-oxo-1-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]butan-2-yl}-L-lysinamide C25 H35 N5 O8 WFSLHCGPTMFRHH-VYJAJWGXSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.725	α = 90
b = 103.725	β = 90
c = 127.189	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Yim, M.K., Schumann, N.C., Goldfarb, N.E., Johnson, S.J.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release
  
• Version 1.1: 2026-04-15
  Changes: Database references