4X1P

The crystal structure of mupain-1-17 in complex with murinised human uPA at pH4.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Distinctive binding modes and inhibitory mechanisms of two peptidic inhibitors of urokinase-type plasminogen activator with isomeric P1 residues.

Jiang, L.Zhao, B.Xu, P.Srensen, H.P.Jensen, J.K.Christensen, A.Hosseini, M.Nielsen, N.C.Jensen, K.J.Andreasen, P.A.Huang, M.

(2015) Int.J.Biochem.Cell Biol. 62: 88-92

  • DOI: 10.1016/j.biocel.2015.02.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two isomeric piperidine derivatives (meta and para isomers) were used as arginine mimics in the P1 position of a cyclic peptidic inhibitor (CPAYSRYLDC) of urokinase-type plasminogen activator. The two resulting cyclic peptides showed vastly different ...

    Two isomeric piperidine derivatives (meta and para isomers) were used as arginine mimics in the P1 position of a cyclic peptidic inhibitor (CPAYSRYLDC) of urokinase-type plasminogen activator. The two resulting cyclic peptides showed vastly different affinities (∼70 fold) to the target enzyme. X-ray crystal structure analysis showed that the two P1 residues were inserted into the S1 specificity pocket in indistinguishable manners. However, the rest of the peptides bound in entirely different ways on the surface of the enzyme, and the two peptides have different conformations, despite the highly similar sequence. These results demonstrate how the subtle difference in P1 residue can dictate the exosite interactions and the potencies of peptidic inhibitors, and highlight the importance of the P1 residue for protease inhibition. This study provides important information for the development of peptidic agents for pharmacological intervention.


    Organizational Affiliation

    Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China(1); Danish-Chinese Centre for Proteases and Cancer, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urokinase-type plasminogen activator
U
247Homo sapiensMutation(s): 3 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Go to Gene View: PLAU
Go to UniProtKB:  P00749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MUPAIN-1-17
P
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRZ
Query on MRZ

Download SDF File 
Download CCD File 
P
piperidine-1-carboximidamide
C6 H13 N3
QUUYRYYUKNNNNS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
U
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
U
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DAL
Query on DAL
P
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 121.082α = 90.00
b = 121.082β = 90.00
c = 43.242γ = 120.00
Software Package:
Software NamePurpose
Cootdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31161130356
National Natural Science Foundation of ChinaChina31170707
the Natural Science Foundation of Fujian ProvinceChina2012J05071
the Danish National Research FoundationDenmark26-331-6

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Author supporting evidence, Derived calculations