9F6C | pdb_00009f6c

Cardiac myosin motor domain in the pre-powerstroke state co-crystallized with the inhibitor aficamten


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.244 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Aficamten is a small-molecule cardiac myosin inhibitor designed to treat hypertrophic cardiomyopathy.

Hartman, J.J.Hwee, D.T.Robert-Paganin, J.Chuang, C.Chin, E.R.Edell, S.Lee, K.H.Madhvani, R.Paliwal, P.Pernier, J.Sarkar, S.S.Schaletzky, J.Schauer, K.Taheri, K.D.Wang, J.Wehri, E.Wu, Y.Houdusse, A.Morgan, B.P.Malik, F.I.

(2024) Nat Cardiovasc Res 3: 1003-1016

  • DOI: https://doi.org/10.1038/s44161-024-00505-0
  • Primary Citation Related Structures: 
    9F6C

  • PubMed Abstract: 

    Hypertrophic cardiomyopathy (HCM) is an inherited disease of the sarcomere resulting in excessive cardiac contractility. The first-in-class cardiac myosin inhibitor, mavacamten, improves symptoms in obstructive HCM. Here we present aficamten, a selective small-molecule inhibitor of cardiac myosin that diminishes ATPase activity by strongly slowing phosphate release, stabilizing a weak actin-binding state. Binding to an allosteric site on the myosin catalytic domain distinct from mavacamten, aficamten prevents the conformational changes necessary to enter the strongly actin-bound force-generating state. In doing so, aficamten reduces the number of functional myosin heads driving sarcomere shortening. The crystal structure of aficamten bound to cardiac myosin in the pre-powerstroke state provides a basis for understanding its selectivity over smooth and fast skeletal muscle. Furthermore, in cardiac myocytes and in mice bearing the hypertrophic R403Q cardiac myosin mutation, aficamten reduces cardiac contractility. Our findings suggest aficamten holds promise as a therapy for HCM.


  • Organizational Affiliation
    • Research and Non-Clinical Development, Cytokinetics, South San Francisco, CA, USA. jhartman@cytokinetics.com.

Macromolecule Content 

  • Total Structure Weight: 180.53 kDa 
  • Atom Count: 11,944 
  • Modeled Residue Count: 1,423 
  • Deposited Residue Count: 1,564 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myosin-7
A, B
782Bos taurusMutation(s): 0 
Gene Names: MYH7
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

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
6I6
(Subject of Investigation/LOI)

Query on 6I6



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
aficamten
C18 H19 N5 O2
IOVAZWDIRCRMTM-OAHLLOKOSA-N
VO4

Query on VO4



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B]
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
H [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: 2.33 Å
  • R-Value Free:  0.244 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.424α = 90
b = 128.326β = 91.47
c = 103.53γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references