Crystal structure of uPA in complex with quercetin

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 

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A structural mechanism of flavonoids in inhibiting serine proteases

Xue, G.Gong, L.Yuan, C.Xu, M.Wang, X.Jiang, L.Huang, M.

(2017) Food Funct 8: 2437-2443

  • DOI: https://doi.org/10.1039/c6fo01825d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Quercetin is a member of the flavonoids and was previously demonstrated to inhibit trypsin-like serine proteases at micromolar potencies. Different molecular models were proposed to explain such inhibition. However, controversies remain on the molecular details of inhibition. Here, we report the X-ray crystal structure of quercetin in a complex with the urokinase-type plasminogen activator (uPA), an archetypical serine protease. The structure showed that quercetin binds to the specific substrate binding pocket (S1 pocket) of uPA mainly through its two neighboring phenolic hydroxyl groups. Our study thus provides unambiguous evidence to support quercetin binding to serine proteases and defines the molecular basis of the interaction. Our results further establish that natural products with two adjacent phenolic hydroxyl groups (or catechol) are likely to inhibit other trypsin-like serine proteases, a new mechanism formerly under-recognized.

  • Organizational Affiliation

    State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China. jianglg@fzu.edu.cn HMD_lab@fzu.edu.cn.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urokinase-type plasminogen activatorA [auth U]246Homo sapiensMutation(s): 0 
Gene Names: PLAU
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
PHAROS:  P00749
GTEx:  ENSG00000122861 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00749
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on QUE

Download Ideal Coordinates CCD File 
C15 H10 O7
Query on PG6

Download Ideal Coordinates CCD File 
C12 H26 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
QUE BindingDB:  5XG4 IC50: min: 1.21e+4, max: 2.00e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.969α = 90
b = 119.969β = 90
c = 41.78γ = 120
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data 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: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description