9ECU | pdb_00009ecu

Crystal structure of the inactive BRAF/MEK1 complex bound to IK-595


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 
    0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The MEK-RAF molecular glue IK-595 has potent antitumor activity across RAS/MAPK pathway-altered cancers.

Haines, E.Burke, M.Catterall, R.De Jesus, V.Hidalgo, D.Li, B.Manna, J.D.Yang, A.Cavanaugh, J.Wessell, S.R.Sanchez-Martin, M.Ivliev, A.Bartolini, W.Santillana, S.Ecsedy, J.Zhang, M.X.Ruppel, S.K.

(2026) Nat Cancer 

  • DOI: https://doi.org/10.1038/s43018-025-01081-3
  • Primary Citation of Related Structures:  
    9ECU

  • PubMed Abstract: 

    MAPK pathway alterations are the most common oncogenic drivers. Among the approved therapies targeting this pathway are RAS, MEK and RAF inhibitors. However, therapeutic resistance and toxicities have limited their clinical success. Here, to overcome these liabilities, we developed IK-595, a potent MEK-RAF molecular glue. IK-595 traps MEK in an inactive complex with all RAF isoforms. In addition, IK-595 precludes CRAF-mediated MEK reactivation and ARAF heterodimerization, allowing for prolonged target engagement and durable MAPK pathway inhibition. This translates into superior antitumor activity across a wide range of cancer model indications harboring MAPK pathway alterations. A key advantage of IK-595 is its ability to achieve transient high plasma exposure affording a larger therapeutic window. The unique mechanism of action and improved tolerability positions IK-595 as an ideal combination partner. IK-595 is an MEK-RAF molecular glue that prolongs pathway inhibition while providing a broader therapeutic window as monotherapy and in combination.


  • Organizational Affiliation
    • Ikena Oncology, Inc., Boston, MA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf284Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
GTEx:  ENSG00000157764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1393Homo sapiensMutation(s): 0 
Gene Names: MAP2K1MEK1PRKMK1
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
PHAROS:  Q02750
GTEx:  ENSG00000169032 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02750
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BIS (Subject of Investigation/LOI)
Query on A1BIS

Download Ideal Coordinates CCD File 
G [auth B]4-[2-chloro-3-(methylsulfamamido)phenoxy]-N-cyclopropyl-2-(2-fluoro-4-iodoanilino)-1,5-dimethyl-6-oxo-1,6-dihydropyridine-3-carboxamide
C24 H24 Cl F I N5 O5 S
RDFUWPLPCIAPFU-UHFFFAOYSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.69α = 90
b = 116.69β = 90
c = 129.87γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2026-01-14 
  • Deposition Author(s): Yang, A.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Database references