6L8L | pdb_00006l8l

C-Src in complex with ibrutinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.286 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Characterization of ibrutinib as a non-covalent inhibitor of SRC-family kinases.

Guo, M.Dai, S.Wu, D.Duan, Y.Li, J.Qu, L.Jiang, L.Chen, Z.Chen, X.Chen, Y.

(2020) Bioorg Med Chem Lett 34: 127757-127757

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127757
  • Primary Citation Related Structures: 
    6L8L

  • PubMed Abstract: 

    Ibrutinib is a BTK-targeted irreversible inhibitor. In this study, we demonstrate that ibrutinib potently inhibits SRC activity in a non-covalent manner via mass spectrometry and crystallography. The S345C mutation renders SRC to bind covalently with ibrutinib, and restores the potency of ibrutinib against the gatekeeper mutant. The co-crystal structure of ibrutinib/SRC shows Ser345 of SRC did not form covalent bond with ibrutinib, leading to a decrease of potency and loss of the ability to overcome the gatekeeper mutation of SRC. The X-ray crystallographic studies also provide structural insight into why ibrutinib behaves differently against gatekeeper mutants of different kinases.


  • Organizational Affiliation
    • Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.

Macromolecule Content 

  • Total Structure Weight: 132.67 kDa 
  • Atom Count: 8,393 
  • Modeled Residue Count: 1,028 
  • Deposited Residue Count: 1,144 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src
A, B, C, D
286Gallus gallusMutation(s): 0 
Gene Names: SRC
EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00523
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.286 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.604α = 89.97
b = 63.407β = 89.94
c = 113.922γ = 90.03
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81372904
National Natural Science Foundation of ChinaChina81570537

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description