35WF | pdb_000035wf

Crystal structure of CHK1 in complex with prexasertib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.204 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 35WF

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of BBI-355, a Potent, Selective, and Orally Available Checkpoint Kinase 1 Inhibitor for the Treatment of Extrachromosomal DNA Oncogene-Amplified Cancers.

Meyer, S.T.Chowdhry, S.Elsdon, R.J.Mauger, J.Truong, Y.P.H.Hansen, R.Plum, J.Steffy, A.Pferdekamper, A.Norman, B.Garcia, S.Tse, E.Apuy, J.Ardeshiri, A.Kasibhatla, S.Hassig, C.A.Pinkerton, A.B.

(2026) J Med Chem 69: 17814-17824

  • DOI: https://doi.org/10.1021/acs.jmedchem.6c00822
  • Primary Citation Related Structures: 
    35WF, 35WG

  • PubMed Abstract: 

    Checkpoint kinase 1 (CHK1), a master regulator of replication stress, has been investigated as a potential therapeutic target for over two decades. More recently, CHK1 has been implicated as a target for the treatment of ecDNA-driven, oncogene-amplified cancers. However, clinical-stage CHK1 inhibitors have historically faced challenges related to dosing schedule, tolerability, and clinical efficacy, although recent studies suggest that biomarker-driven approaches and alternative dosing strategies may address some of these limitations. Structure-guided optimization led to the discovery of BBI-355, a potent, selective, and orally available CHK1 inhibitor. BBI-355 demonstrates strong antitumor activity when dosed orally in mouse xenograft models, achieving regressions both as a single agent and in combination with targeted therapies. BBI-355 also displays favorable ADMET and PK properties and has been advanced to a clinical trial for patients with oncogene amplified cancers.


  • Organizational Affiliation
    • Boundless Bio, Inc, 10955 Alexandria Way Suite 100, San Diego, California 92121, United States.

Macromolecule Content 

  • Total Structure Weight: 34.42 kDa 
  • Atom Count: 2,800 
  • Modeled Residue Count: 277 
  • Deposited Residue Count: 280 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1280Homo sapiensMutation(s): 0 
Gene Names: CHEK1CHK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
GTEx:  ENSG00000149554 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1DNH
(Subject of Investigation/LOI)

Query on A1DNH



Download:Ideal Coordinates CCD File
B [auth A]prexasertib
C18 H19 N7 O2
DOTGPNHGTYJDEP-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
T [auth A]
U [auth A]
V [auth A]
W [auth A]
X [auth A]
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH

Query on EOH



Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
N [auth A]
O [auth A]
P [auth A]
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.204 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.4α = 90
b = 64.82β = 102.77
c = 53.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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: 2026-08-05
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Database references