1H7X

Dihydropyrimidine dehydrogenase (DPD) from pig, ternary complex of a mutant enzyme (C671A), NADPH and 5-fluorouracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Crystal Structure of Dihydropyrimidine Dehydrogenase, a Major Determinant of the Pharmacokinetics of the Anti-Cancer Drug 5-Fluorouracil

Dobritzsch, D.Schneider, G.Schnackerz, K.D.Lindqvist, Y.

(2001) EMBO J 20: 650

  • DOI: https://doi.org/10.1093/emboj/20.4.650
  • Primary Citation of Related Structures:  
    1H7W, 1H7X

  • PubMed Abstract: 

    Dihydropyrimidine dehydrogenase catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. Its controlled inhibition has become an adjunct target for cancer therapy, since the enzyme is also responsible for the rapid breakdown of the chemotherapeutic drug 5-fluorouracil. The crystal structure of the homodimeric pig liver enzyme (2x 111 kDa) determined at 1.9 A resolution reveals a highly modular subunit organization, consisting of five domains with different folds. Dihydropyrimidine dehydrogenase contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue. The ternary complex of an inactive mutant of the enzyme with bound NADPH and 5-fluorouracil reveals the architecture of the substrate-binding sites and residues responsible for recognition and binding of the drug.


  • Organizational Affiliation

    Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIHYDROPYRIMIDINE DEHYDROGENASE
A, B, C, D
1,025Sus scrofaMutation(s): 1 
Gene Names: DPYD
EC: 1.3.1.2
UniProt
Find proteins for Q28943 (Sus scrofa)
Explore Q28943 
Go to UniProtKB:  Q28943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ28943
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
HA [auth D],
J [auth A],
R [auth B],
Z [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
AA [auth C],
IA [auth D],
K [auth A],
S [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
GA [auth D],
I [auth A],
Q [auth B],
Y [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
E [auth A]
EA [auth D]
F [auth A]
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
URF
Query on URF

Download Ideal Coordinates CCD File 
BA [auth C],
JA [auth D],
L [auth A],
T [auth B]
5-FLUOROURACIL
C4 H3 F N2 O2
GHASVSINZRGABV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.95α = 90
b = 159.29β = 96.04
c = 163.57γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-01-17
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2018-02-07
    Changes: Source and taxonomy
  • Version 2.2: 2024-05-01
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description