8QYU

Beta-cardiac myosin S1 fragment in the pre-powerstroke state complexed to Omecamtiv mecarbil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5N69


Literature

Omecamtiv mecarbil and Mavacamten target the same myosin pocket despite antagonistic effects in heart contraction.

Auguin, D.Robert-Paganin, J.Rety, S.Kikuti, C.David, A.Theumer, G.Schmidt, A.W.Knolker, H.J.Houdusse, A.

(2023) Biorxiv 

  • DOI: https://doi.org/10.1101/2023.11.15.567213
  • Primary Citation of Related Structures:  
    8QYP, 8QYQ, 8QYR, 8QYU

  • PubMed Abstract: 

    Inherited cardiomyopathies are amongst the most common cardiac diseases worldwide, leading in the late-stage to heart failure and death. The most promising treatments against these diseases are small-molecules directly modulating the force produced by β-cardiac myosin, the molecular motor driving heart contraction. Two of these molecules that produce antagonistic effects on cardiac contractility have completed clinical phase 3 trials: the activator Omecamtiv mecarbil and the inhibitor Mavacamten . In this work, we reveal by X-ray crystallography that both drugs target the same pocket and stabilize a pre-stroke structural state, with only few local differences. All atoms molecular dynamics simulations reveal how these molecules can have antagonistic impact on the allostery of the motor by comparing β-cardiac myosin in the apo form or bound to Omecamtiv mecarbil or Mavacamten . Altogether, our results provide the framework for rational drug development for the purpose of personalized medicine.


  • Organizational Affiliation

    Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258 Paris cedex 05, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myosin-7
A, B
810Bos taurusMutation(s): 0 
UniProt
Find proteins for Q9BE39 (Bos taurus)
Explore Q9BE39 
Go to UniProtKB:  Q9BE39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BE39
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Myosin light chain 3C [auth G],
D [auth H]
199Bos taurusMutation(s): 0 
UniProt
Find proteins for P85100 (Bos taurus)
Explore P85100 
Go to UniProtKB:  P85100
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP85100
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
2OW (Subject of Investigation/LOI)
Query on 2OW

Download Ideal Coordinates CCD File 
L [auth A],
V [auth B]
methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate
C20 H24 F N5 O3
RFUBTTPMWSKEIW-UHFFFAOYSA-N
VO4 (Subject of Investigation/LOI)
Query on VO4

Download Ideal Coordinates CCD File 
F [auth A],
N [auth B]
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
MLA
Query on MLA

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U [auth B]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
S [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
R [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
P [auth B],
Q [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
O [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
A, B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.996α = 90
b = 122.503β = 90
c = 187.463γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The French Muscular Dystrophy Telethon (AFM-Telethon)France21805
Fondation pour la Recherche Medicale (FRM)FranceDCM20181039553
Agence Nationale de la Recherche (ANR)France21-CE11-0022-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRM1GM131981-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release