8QYQ | pdb_00008qyq

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 230.51 kDa 
  • Atom Count: 14,993 
  • Modeled Residue Count: 1,793 
  • Deposited Residue Count: 2,012 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myosin-7
A, B
807Bos 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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Myosin light chain 3199Bos 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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Myosin light chain 3199Bos 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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
XB2
(Subject of Investigation/LOI)

Query on XB2



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
Mavacamten
C15 H19 N3 O2
RLCLASQCAPXVLM-NSHDSACASA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
R [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BEF
(Subject of Investigation/LOI)

Query on BEF



Download:Ideal Coordinates CCD File
F [auth A],
M [auth B]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
FMT

Query on FMT



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [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],
Q [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: 2.61 Å
  • R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.801α = 90
b = 147.977β = 91.62
c = 116.751γ = 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
  • Version 1.1: 2025-11-12
    Changes: Derived calculations, Structure summary