6OCW

Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor A85


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Selective Phenylimidazole-Based Inhibitors of theMycobacterium tuberculosisProteasome.

Zhan, W.Hsu, H.C.Morgan, T.Ouellette, T.Burns-Huang, K.Hara, R.Wright, A.G.Imaeda, T.Okamoto, R.Sato, K.Michino, M.Ramjee, M.Aso, K.Meinke, P.T.Foley, M.Nathan, C.F.Li, H.Lin, G.

(2019) J.Med.Chem. 62: 9246-9253

  • DOI: 10.1021/acs.jmedchem.9b01187
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, <i>Mycobacterium tuberculosis </i> (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genet ...

    Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders nonreplicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial over human proteasomes.


    Organizational Affiliation

    Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States.,Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States.,Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K.,Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha
A, B, C, D, E, F, G, O, P, Q, R, S, T, U
240Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcA
EC: 3.4.25.1
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHU1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta
H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
234Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcB
EC: 3.4.25.1
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHT9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
a, b, H, I, J, K, L, M, N, V, W, X, Y, Z
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
M6M
Query on M6M

Download SDF File 
Download CCD File 
a, b, H, I, J, K, L, M, N, V, W, X, Y, Z
N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-4-[(2S)-2-methylpiperidin-1-yl]-1,4-dioxobutan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name)
C25 H31 F2 N5 O5
XOTJQAONWIKZEB-UVFQYZLESA-N
 Ligand Interaction
DMF
Query on DMF

Download SDF File 
Download CCD File 
a, A, C, D, E, F, J, O, P, Q, R, S, T, U
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 120.183α = 90.00
b = 198.647β = 103.58
c = 166.355γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-25 
  • Released Date: 2019-10-09 
  • Deposition Author(s): Hsu, H.C., Li, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI070285

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references
  • Version 1.2: 2019-11-06
    Type: Data collection, Database references
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence