8TCE

Lipoprotein(a) Kringle IV domain 8 - Lp(a) KIV8 in complex with LY3353871


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of potent small-molecule inhibitors of lipoprotein(a) formation.

Diaz, N.Perez, C.Escribano, A.M.Sanz, G.Priego, J.Lafuente, C.Barberis, M.Calle, L.Espinosa, J.F.Priest, B.T.Zhang, H.Y.Nosie, A.K.Haas, J.V.Cannady, E.Borel, A.Schultze, A.E.Sauder, J.M.Hendle, J.Weichert, K.Nicholls, S.J.Michael, L.F.

(2024) Nature 629: 945-950

  • DOI: https://doi.org/10.1038/s41586-024-07387-z
  • Primary Citation of Related Structures:  
    8TCE, 8V8Z, 8V9B

  • PubMed Abstract: 

    Lipoprotein(a) (Lp(a)), an independent, causal cardiovascular risk factor, is a lipoprotein particle that is formed by the interaction of a low-density lipoprotein (LDL) particle and apolipoprotein(a) (apo(a)) 1,2 . Apo(a) first binds to lysine residues of apolipoprotein B-100 (apoB-100) on LDL through the Kringle IV (K IV ) 7 and 8 domains, before a disulfide bond forms between apo(a) and apoB-100 to create Lp(a) (refs. 3-7 ). Here we show that the first step of Lp(a) formation can be inhibited through small-molecule interactions with apo(a) K IV 7-8. We identify compounds that bind to apo(a) K IV 7-8, and, through chemical optimization and further application of multivalency, we create compounds with subnanomolar potency that inhibit the formation of Lp(a). Oral doses of prototype compounds and a potent, multivalent disruptor, LY3473329 (muvalaplin), reduced the levels of Lp(a) in transgenic mice and in cynomolgus monkeys. Although multivalent molecules bind to the Kringle domains of rat plasminogen and reduce plasmin activity, species-selective differences in plasminogen sequences suggest that inhibitor molecules will reduce the levels of Lp(a), but not those of plasminogen, in humans. These data support the clinical development of LY3473329-which is already in phase 2 studies-as a potent and specific orally administered agent for reducing the levels of Lp(a).


  • Organizational Affiliation

    Lilly Research Laboratories, Alcobendas, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein(a)
A, B
94Homo sapiensMutation(s): 0 
Gene Names: LPA
UniProt & NIH Common Fund Data Resources
Find proteins for P08519 (Homo sapiens)
Explore P08519 
Go to UniProtKB:  P08519
PHAROS:  P08519
GTEx:  ENSG00000198670 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08519
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HWF (Subject of Investigation/LOI)
Query on HWF

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S)-3-phenyl-2-[(3R)-pyrrolidin-3-yl]propanoic acid
C13 H17 N O2
OSTNIMGVYREMID-RYUDHWBXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.602α = 90
b = 57.574β = 94.7
c = 38.305γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references