8XHM | pdb_00008xhm

Crystal structure of Nocardia seriolae dUTP diphosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Structure-guided discovery of novel dUTPase inhibitors with anti- Nocardia activity by computational design.

Wang, Z.Z.Weng, J.Qi, J.Fu, X.X.Xing, B.B.Hu, Y.Huang, C.H.Chen, C.Y.Wei, Z.

(2024) J Enzyme Inhib Med Chem 39: 2411573-2411573

  • DOI: https://doi.org/10.1080/14756366.2024.2411573
  • Primary Citation Related Structures: 
    8XHM

  • PubMed Abstract: 

    The zoonosis caused by Nocardia is increasing seriously. But commonly used antibiotic drugs often lead to resistance. N. seriolae dUTPase ( Ns dUTPase) plays a key role in the proliferation of Nocardia , and was regarded as a potent drug target. However, there was little report about the Ns dUTPase inhibitors. In this study, we discovered a series of novel Ns dUTPase inhibitors to fight against Nocardia . The first crystal structure of Ns dUTPase was released, and a structure-based computational design was performed. Compounds 4b and 12b exhibited promising activities towards Ns dUTPase (IC 50  = 0.99 μM and 0.7 μM). In addition, they showed satisfied anti- Nocardia activity (MIC value ranges from 0.5 to 2 mg/L) and low cytotoxicity, which were better than approved drugs oxytetracycline and florfenicol. Molecular modelling study indicated that hydrophobic interaction might be the main contribution for ligand binding. Our results suggested that Ns dUTPase inhibitors might be a useful way to repress Nocardia .


  • Organizational Affiliation
    • School of Life Sciences, State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, Hubei University, Wuhan, PR China.

Macromolecule Content 

  • Total Structure Weight: 20.56 kDa 
  • Atom Count: 1,127 
  • Modeled Residue Count: 140 
  • Deposited Residue Count: 194 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase194Nocardia seriolaeMutation(s): 0 
Gene Names: dutD6158_15615NS07_v2contig00045-0031NS506_05871
EC: 3.6.1.23

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UMP
(Subject of Investigation/LOI)

Query on UMP



Download:Ideal Coordinates CCD File
B [auth A]2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
D [auth A],
G [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



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

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.807α = 90
b = 120.807β = 90
c = 120.807γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaSKLBEE2022007

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release