8XJJ | pdb_00008xjj

Co-crystal structure of SOS-1 and a potent, selective and orally bioavailable SOS1 inhibitor RGT-018


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.264 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8XJJ

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of RGT-018: A Potent, Selective, and Orally Bioavailable SOS1 Inhibitor for KRAS-Driven Cancers.

Xiao, F.Wang, K.Wang, X.Li, H.Hu, Z.Ren, X.Huang, W.Feng, T.Yao, L.Lin, J.Li, C.Zhang, Z.Mei, L.Zhu, X.Zhong, W.Xie, Z.

(2024) Mol Cancer Ther 23: 1703-1716

  • DOI: https://doi.org/10.1158/1535-7163.MCT-24-0049
  • Primary Citation Related Structures: 
    8XJJ

  • PubMed Abstract: 

    KRAS is the most frequently dysregulated oncogene with high prevalence in NSCLC, colorectal cancer, and pancreatic cancer. FDA-approved sotorasib and adagrasib provide breakthrough therapies for cancer patients with KRASG12C mutation. However, there is still high unmet medical need for new agents targeting broader KRAS-driven tumors. An emerging and promising opportunity is to develop a pan KRAS inhibitor by suppressing the upstream protein SOS1. SOS1 is a key activator of KRAS and facilitates the conversion of GDP-bound KRAS state to GTP-bound KRAS state. Binding to its catalytic domain, small molecule SOS1 inhibitor has demonstrated the ability to suppress KRAS activation and cancer cell proliferation. RGT-018, a potent and selective SOS1 inhibitor, was identified with optimal drug-like properties. In vitro, RGT-018 blocked the interaction of KRAS:SOS1 with single digit nM potency and is highly selective against SOS2. RGT-018 inhibited KRAS signaling and the proliferation of a broad spectrum of KRAS-driven cancer cells as a single agent in vitro. Further enhanced anti-proliferation activity was observed when RGT-018 was combined with MEK, KRASG12C, EGFR or CDK4/6 inhibitors. Oral administration of RGT-018 inhibited tumor growth and suppressed KRAS signaling in tumor xenografts in vivo. Combination with MEK or KRASG12C inhibitors led to significant tumor regression. Furthermore, RGT-018 overcame the resistance to the approved KRASG12C inhibitors caused by clinically acquired KRAS mutations either as a single agent or in combination. RGT-018 displayed promising pharmacological properties for combination with targeted agents to treat a broader KRAS-driven patient population.


  • Organizational Affiliation
    • Regor Therapeutics Group, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 69.27 kDa 
  • Atom Count: 4,109 
  • Modeled Residue Count: 473 
  • Deposited Residue Count: 590 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Son of sevenless homolog 1590Homo sapiensMutation(s): 4 
Gene Names: SOS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
PHAROS:  Q07889
GTEx:  ENSG00000115904 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07889
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LVJ
(Subject of Investigation/LOI)

Query on A1LVJ



Download:Ideal Coordinates CCD File
B [auth A]5-[4-[[(1~{R})-1-[3-[bis(fluoranyl)methyl]-2-fluoranyl-phenyl]ethyl]amino]-2-methyl-6-morpholin-4-yl-7-oxidanylidene-pyrido[4,3-d]pyrimidin-8-yl]pyridine-2-carbonitrile
C27 H24 F3 N7 O2
HRMKBFIINYRRDO-OAHLLOKOSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.264 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.76α = 90
b = 83.85β = 90
c = 179.02γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-08-14 
  • Deposition Author(s): Ren, X.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references, Structure summary