5E93

Crystal Structure of Trypanosoma cruzi Dihydroorotate Dehydrogenase in Complex with Neq0071


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Exploring Trypanosoma cruzi Dihydroorotate Dehydrogenase Active Site Plasticity for the Discovery of Potent and Selective Inhibitors with Trypanocidal Activity

Rocha, J.R.Cheleski, J.Inaoka, D.K.Avelar, L.A.Ribeiro, J.F.R.Wiggers, H.J.Albuquerque, S.Shiba, T.Harada, S.Kita, K.Silva, A.B.F.Montanari, C.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (fumarate)
A, B
314Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: PyrDpyr4
EC: 1.3.98.1
UniProt
Find proteins for Q4D3W2 (Trypanosoma cruzi (strain CL Brener))
Explore Q4D3W2 
Go to UniProtKB:  Q4D3W2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4D3W2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
FA [auth B],
J [auth A]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
5LL
Query on 5LL

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C [auth A],
Y [auth B]
5-[(E)-3-(furan-2-yl)prop-2-enylidene]-1,3-diazinane-2,4,6-trione
C11 H8 N2 O4
PRGJOMANJQAXIH-HNQUOIGGSA-N
NCO
Query on NCO

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GA [auth B],
HA [auth B],
K [auth A]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
CAC
Query on CAC

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W [auth A],
X [auth A]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
PEG
Query on PEG

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UA [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
IA [auth B]
JA [auth B]
KA [auth B]
L [auth A]
LA [auth B]
IA [auth B],
JA [auth B],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
V [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.325α = 90
b = 71.789β = 90
c = 124.343γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Creative Scientific ResearchJapan18GS0314
Japanese Society for the Promotion of ScienceJapan18073004, 26253025, 26870119
Science and Technology Research Partnership for Sustainable DevelopmentJapan10000284
Fundacao de Amparo a Pesquisa do Estado de Sao PauloBrazil2010/20021-4, 2012/01777-6

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations