5URS | pdb_00005urs

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P178


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.279 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5URS

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections.

Modi, G.Marqus, G.M.Vippila, M.R.Gollapalli, D.R.Kim, Y.Manna, A.C.Chacko, S.Maltseva, N.Wang, X.Cullinane, R.T.Zhang, Y.Kotler, J.L.M.Kuzmic, P.Zhang, M.Lawson, A.P.Joachimiak, A.Cheung, A.Snider, B.B.Rothstein, D.M.Cuny, G.D.Hedstrom, L.

(2021) ACS Infect Dis 7: 3062-3076

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00342
  • Primary Citation Related Structures: 
    5URS, 5UUV, 5UUZ, 7MTU, 7MTX

  • PubMed Abstract: 

    Many bacterial pathogens, including Staphylococcus aureus , require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH ( Sa IMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. Five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro . Resistance resulted from substitutions in the cofactor/inhibitor binding site of Sa IMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive Sa IMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of Sa IMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may be responsible for its role in infection.


  • Organizational Affiliation
    • Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States.

Macromolecule Content 

  • Total Structure Weight: 333.14 kDa 
  • Atom Count: 21,357 
  • Modeled Residue Count: 2,798 
  • Deposited Residue Count: 3,072 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
384Bacillus anthracisMutation(s): 0 
Gene Names: guaBGBAA_0008A8C77_00065ABW01_29210
EC: 1.1.1.205
UniProt
Find proteins for A0A6L8P2U9 (Bacillus anthracis)
Explore A0A6L8P2U9 
Go to UniProtKB:  A0A6L8P2U9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L8P2U9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8LA

Query on 8LA



Download:Ideal Coordinates CCD File
FA [auth F]
IA [auth G]
J [auth A]
LA [auth H]
O [auth B]
FA [auth F],
IA [auth G],
J [auth A],
LA [auth H],
O [auth B],
R [auth C],
W [auth D],
Z [auth E]
N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea
C24 H29 Cl N2 O6
DGCHEIBDGDMRPM-YSFYHYPLSA-N
IMP

Query on IMP



Download:Ideal Coordinates CCD File
EA [auth F]
HA [auth G]
I [auth A]
KA [auth H]
N [auth B]
EA [auth F],
HA [auth G],
I [auth A],
KA [auth H],
N [auth B],
Q [auth C],
V [auth D],
Y [auth E]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
BA [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
CA [auth E],
S [auth C],
T [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
X [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
AA [auth E]
DA [auth E]
GA [auth F]
JA [auth G]
K [auth A]
AA [auth E],
DA [auth E],
GA [auth F],
JA [auth G],
K [auth A],
M [auth A],
P [auth B],
U [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.345α = 98.71
b = 89.581β = 89.82
c = 104.158γ = 96.69
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing

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 General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Structure summary
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2026-03-25
    Changes: Database references, Structure summary