5UGG

Protease Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

X-ray crystal structure of plasmin with tranexamic acid-derived active site inhibitors.

Law, R.H.P.Wu, G.Leung, E.W.W.Hidaka, K.Quek, A.J.Caradoc-Davies, T.T.Jeevarajah, D.Conroy, P.J.Kirby, N.M.Norton, R.S.Tsuda, Y.Whisstock, J.C.

(2017) Blood Adv 1: 766-771

  • DOI: 10.1182/bloodadvances.2016004150
  • Primary Citation of Related Structures:  
    5UGD, 5UGG

  • PubMed Abstract: 
  • The zymogen protease plasminogen and its active form plasmin perform key roles in blood clot dissolution, tissue remodeling, cell migration, and bacterial pathogenesis. Dysregulation of the plasminogen/plasmin system results in life-threatening hemorrhagic disorders or thrombotic vascular occlusion ...

    The zymogen protease plasminogen and its active form plasmin perform key roles in blood clot dissolution, tissue remodeling, cell migration, and bacterial pathogenesis. Dysregulation of the plasminogen/plasmin system results in life-threatening hemorrhagic disorders or thrombotic vascular occlusion. Accordingly, inhibitors of this system are clinically important. Currently, tranexamic acid (TXA), a molecule that prevents plasminogen activation through blocking recruitment to target substrates, is the most widely used inhibitor for the plasminogen/plasmin system in therapeutics. However, TXA lacks efficacy on the active form of plasmin. Thus, there is a need to develop specific inhibitors that target the protease active site. Here we report the crystal structures of plasmin in complex with the novel YO ( trans -4-aminomethylcyclohexanecarbonyl-l-tyrosine- n -octylamide) class of small molecule inhibitors. We found that these inhibitors form key interactions with the S1 and S3' subsites of the catalytic cleft. Here, the TXA moiety of the YO compounds inserts into the primary (S1) specificity pocket, suggesting that TXA itself may function as a weak plasmin inhibitor, a hypothesis supported by subsequent biochemical and biophysical analyses. Mutational studies reveal that F587 of the S' subsite plays a key role in mediating the inhibitor interaction. Taken together, these data provide a foundation for the future development of small molecule inhibitors to specifically regulate plasmin function in a range of diseases and disorders.


    Organizational Affiliation

    Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PlasminogenA251Homo sapiensMutation(s): 0 
Gene Names: PLG
EC: 3.4.21.7
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens)
Explore P00747 
Go to UniProtKB:  P00747
PHAROS:  P00747
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00747
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
89M
Query on 89M

Download Ideal Coordinates CCD File 
B [auth A]Nalpha-[trans-4-(aminomethyl)cyclohexane-1-carbonyl]-N-octyl-O-[(quinolin-2-yl)methyl]-L-tyrosinamide
C35 H48 N4 O3
ZGUNTZKJIWJKEH-GSZYCOFVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
89M BindingDB:  5UGG IC50: min: 220, max: 380 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.55α = 90
b = 39.48β = 111.88
c = 62.13γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1029403

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2018-01-17
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence