4PA0

Omecamtiv Mercarbil binding site on the Human Beta-Cardiac Myosin Motor Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis for drug-induced allosteric changes to human beta-cardiac myosin motor activity.

Winkelmann, D.A.Forgacs, E.Miller, M.T.Stock, A.M.

(2015) Nat Commun 6: 7974-7974

  • DOI: https://doi.org/10.1038/ncomms8974
  • Primary Citation of Related Structures:  
    4PA0

  • PubMed Abstract: 

    Omecamtiv Mecarbil (OM) is a small molecule allosteric effector of cardiac myosin that is in clinical trials for treatment of systolic heart failure. A detailed kinetic analysis of cardiac myosin has shown that the drug accelerates phosphate release by shifting the equilibrium of the hydrolysis step towards products, leading to a faster transition from weak to strong actin-bound states. The structure of the human β-cardiac motor domain (cMD) with OM bound reveals a single OM-binding site nestled in a narrow cleft separating two domains of the human cMD where it interacts with the key residues that couple lever arm movement to the nucleotide state. In addition, OM induces allosteric changes in three strands of the β-sheet that provides the communication link between the actin-binding interface and the nucleotide pocket. The OM-binding interactions and allosteric changes form the structural basis for the kinetic and mechanical tuning of cardiac myosin.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myosin-7,Green fluorescent protein
A, B
1,024Homo sapiensAequorea victoria
This entity is chimeric
Mutation(s): 6 
Gene Names: MYH7MYHCBGFP
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for P12883 (Homo sapiens)
Explore P12883 
Go to UniProtKB:  P12883
PHAROS:  P12883
GTEx:  ENSG00000092054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP12883P42212
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
A, B
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Binding Affinity Annotations 
IDSourceBinding Affinity
2OW Binding MOAD:  4PA0 Ki: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.167α = 90
b = 88.924β = 93.92
c = 137.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States10GRNT4300022

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection