8BI2 | pdb_00008bi2

Syk kinase domain in complex with macrocyclic inhibitor 20a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.235 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8BI2

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Optimization of a series of novel, potent and selective Macrocyclic SYK inhibitors.

Grimster, N.P.Gingipalli, L.Balazs, A.Barlaam, B.Boiko, S.Boyd, S.Dry, H.Goldberg, F.W.Ikeda, T.Johnson, T.Kawatkar, S.Kemmitt, P.Lamont, S.Lorthioir, O.Mfuh, A.Patel, J.Pike, A.Read, J.Romero, R.Sarkar, U.Sha, L.Simpson, I.Song, K.Su, Q.Wang, H.Watson, D.Wu, A.Zehnder, T.E.Zheng, X.Li, S.Dong, Z.Yang, D.Song, Y.Wang, P.Liu, X.Dowling, J.E.Edmondson, S.D.

(2023) Bioorg Med Chem Lett 91: 129352-129352

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129352
  • Primary Citation Related Structures: 
    8BI2

  • PubMed Abstract: 

    Spleen tyrosine kinase (SYK) is a non-receptor cytoplasmic kinase. Due to its pivotal role in B cell receptor and Fc-receptor signalling, inhibition of SYK has been a target of interest in a variety of diseases. Herein, we report the use of structure-based drug design to discover a series of potent macrocyclic inhibitors of SYK, with excellent kinome selectivity and in vitro metabolic stability. We were able to remove hERG inhibition through the optimization of physical properties, and utilized a pro-drug strategy to address permeability challenges.


  • Organizational Affiliation
    • Oncology R & D, AstraZeneca, Waltham, USA. Electronic address: neil.grimster@astrazeneca.com.

Macromolecule Content 

  • Total Structure Weight: 35.34 kDa 
  • Atom Count: 2,284 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 299 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK299Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
GTEx:  ENSG00000165025 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QR7
(Subject of Investigation/LOI)

Query on QR7



Download:Ideal Coordinates CCD File
B [auth A]10,13,23-trimethyl-16-oxa-2,4,8,9,13,19,23,30-octazapentacyclo[19.5.2.1^{3,7}.1^{8,11}.0^{24,28}]triaconta-1(27),3,5,7(30),9,11(29),21,24(28),25-nonaen-20-one
C24 H28 N8 O2
RKIOUVNEIPKSRD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.235 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.99α = 90
b = 84.985β = 90
c = 90.125γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description