Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 300.19 kDa 
• Atom Count: 22610 
• Residue Count: 2595 
• Unique protein chains: 1

1VDV

Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form

• DOI: 10.2210/pdb1VDV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2004-03-25 Released: 2004-12-21 
• Deposition Author(s): Fukunari, A., Okamoto, K., Nishino, T., Eger, B.T., Pai, E.F., Kamezawa, M., Yamada, I., Kato, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.215 
• R-Value Work: 0.178 

Literature

Y-700 [1-[3-Cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid]: a potent xanthine oxidoreductase inhibitor with hepatic excretion

Fukunari, A., Okamoto, K., Nishino, T., Eger, B.T., Pai, E.F., Kamezawa, M., Yamada, I., Kato, N.

(2004) J Pharmacol Exp Ther 311: 519-528

• PubMed: 15190124 
• DOI: 10.1124/jpet.104.070433
• Primary Citation of Related Structures:  
  1VDV


• PubMed Abstract: 
  

Y-700 (1-[3-Cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid) is a newly synthesized inhibitor of xanthine oxidoreductase (XOR). Steady-state kinetics with the bovine milk enzyme indicated a mixed type inhibition with K(i) and K(i) ' values of 0.6 and 3.2 nM, respectively. Titration experiments showed that Y-700 bound tightly both to the active sulfo-form and to the inactive desulfo-form of the enzyme with K(d) values of 0.9 and 2.8 nM, respectively. X-ray crystallographic analysis of the enzyme-inhibitor complex revealed that Y-700 closely interacts with the channel leading to the molybdenum-pterin active site but does not directly coordinate to the molybdenum ion. In oxonate-treated rats, orally administered Y-700 (1-10 mg/kg) dose dependently lowered plasma urate levels. At a dose of 10 mg/kg, the hypouricemic action of Y-700 was more potent and of longer duration than that of 4-hydroxypyrazolo(3,4-d)pyrimidine, whereas its action was approximately equivalent to that of 2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazolecarboxylic acid, a nonpurine inhibitor of XOR. In normal rats, orally administered Y-700 (0.3-3 mg/kg) dose dependently reduced the urinary excretion of urate and allantoin, accompanied by an increase in the excretion of hypoxanthine and xanthine. Y-700 (1 mg/kg) was absorbed rapidly by the oral route with high bioavailability (84.1%). Y-700 was hardly excreted via the kidneys but was mainly cleared via the liver. These results suggest that Y-700 will be a promising candidate for the treatment of hyperuricemia and other diseases in which XOR may be involved.

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Organizational Affiliation: 

Discovery Technology Laboratory, Pharmaceuticals Research Unit, Mitsubishi Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthine dehydrogenase/oxidase	A, B	1332	Bos taurus	Mutation(s): 0  Gene Names: XDH EC: 1.1.1.204 (PDB Primary Data), 1.17.1.4 (UniProt), 1.17.3.2 (UniProt)
Find proteins for P80457 (Bos taurus) Explore P80457  Go to UniProtKB:  P80457

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MTE	A, B	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER C10 H14 N5 O6 P S2 HPEUEJRPDGMIMY-IFQPEPLCSA-N
YSH	A, B	1-[3-CYANO-4-(NEOPENTYLOXY)PHENYL]-1H-PYRAZOLE-4-CARBOXYLIC ACID C16 H17 N3 O3 AETHRPHBGJAIBT-UHFFFAOYSA-N
FES	A, B	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS	A, B	DIOXOTHIOMOLYBDENUM(VI) ION H Mo O2 S BDSRWPHSAKXXRG-UHFFFAOYSA-M
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	A, B	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
YSH	IC50:  3.5   nM  BindingDB
YSH	IC50:  5.800000190734863   nM  BindingDB
YSH	IC50:  16   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.215 
• R-Value Work: 0.178 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.817	α = 90
b = 123.94	β = 91.16
c = 148.888	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-25 
• Released Date: 2004-12-21 
Deposition Author(s): Fukunari, A., Okamoto, K., Nishino, T., Eger, B.T., Pai, E.F., Kamezawa, M., Yamada, I., Kato, N.

Revision History 

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance