6OCZ

Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor A86


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/acs.jmedchem.9b01187
  • Primary Citation of Related Structures:  
    6OCW, 6OCZ, 6ODE

  • PubMed Abstract: 

    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

    Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha
A, B, C, D, E
A, B, C, D, E, F, G, O, P, Q, R, S, T, U
240Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: prcARv2109c
EC: 3.4.25.1
UniProt
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHU1 
Go to UniProtKB:  P9WHU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHU1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta234Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: prcBRv2110c
EC: 3.4.25.1
UniProt
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHT9 
Go to UniProtKB:  P9WHT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHT9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M6Y
Query on M6Y

Download Ideal Coordinates CCD File 
KA [auth H]
KB [auth V]
MA [auth I]
MB [auth W]
OB [auth X]
KA [auth H],
KB [auth V],
MA [auth I],
MB [auth W],
OB [auth X],
PA [auth J],
QB [auth Y],
SB [auth Z],
TA [auth K],
UB [auth a],
VA [auth L],
WB [auth b],
XA [auth M],
ZA [auth N]
N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name)
C29 H31 F2 N5 O5
ZUCKFGZJAOBNRP-VVMVZBAXSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
AB [auth N]
LA [auth H]
LB [auth V]
NA [auth I]
NB [auth W]
AB [auth N],
LA [auth H],
LB [auth V],
NA [auth I],
NB [auth W],
PB [auth X],
QA [auth J],
RB [auth Y],
TB [auth Z],
UA [auth K],
VB [auth a],
WA [auth L],
XB [auth b],
YA [auth M]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
DMF
Query on DMF

Download Ideal Coordinates CCD File 
BB [auth O]
CA [auth A]
CB [auth P]
DA [auth B]
DB [auth Q]
BB [auth O],
CA [auth A],
CB [auth P],
DA [auth B],
DB [auth Q],
EA [auth C],
EB [auth R],
FA [auth E],
FB [auth R],
GA [auth F],
GB [auth S],
HA [auth F],
HB [auth S],
IA [auth G],
IB [auth T],
JA [auth G],
JB [auth U],
OA [auth I],
RA [auth J],
SA [auth J]
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.768α = 90
b = 198.062β = 103.72
c = 167.919γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references