9IT5 | pdb_00009it5

p300 KAT domain in complex with KB528


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.238 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.194 (DCC) 

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

Catalytic Inhibition of p300 Preferentially Targets IRF4 Oncogenic Activity and Tumor Growth in Multiple Myeloma.

Lenoir, W.F.McKeown, M.R.Giorgetti, G.Kobylarz, M.J.Hopkins, T.D.Glore, W.L.Shum, M.G.Calderon, Y.Encinas Mayoral, J.Carvajal, L.A.Mori, K.R.Li, J.Gao, H.Zheng, Y.Ma, Z.Obholzer, N.D.Zhou, M.Trotter, B.W.Dinsmore, C.J.Munshi, N.C.Lin, C.Y.Fulciniti, M.Rahl, P.B.

(2025) Cancer Res 

  • DOI: https://doi.org/10.1158/0008-5472.CAN-25-3440
  • Primary Citation of Related Structures:  
    9IT5

  • PubMed Abstract: 

    The oncogenic transcription factor (TF) IRF4 is a currently undrugged universal multiple myeloma (MM) dependency. Using transcriptional regulatory network (TRN) mapping, an unbiased multi-omic target ID approach, we identified the coactivator lysine acetyltransferase (KAT) p300 as a key IRF4 partner. Validation of this preferential relationship through quantitative interactome mapping revealed that IRF4 was the most abundant MM specific dependency and more closely complexed with p300 than other TFs, such as IKZF1/IKZF3. Development of optimized p300 lysine acetyltransferase (KAT) inhibitors enabled inhibition of IRF4 activity and MM proliferation ex vivo and in vivo. p300/CBP KAT inhibition preferentially targeted MM cells over normal cells, specifically modulating the MM transcriptome, and the p300 KAT inhibitors more completely inhibited IRF4 activity at lower levels compared to existing p300/CBP bromodomain inhibitors. Furthermore, combining p300/CBP KAT inhibition and therapeutics with orthogonal mechanisms targeting transcription in MM elicited synergistic anti-tumor effects. Together, these data motivate the ongoing clinical development of p300/CBP KAT inhibition in MM.


  • Organizational Affiliation
    • Kronos Bio, Cambridge, MA, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase p300
A, B
349Homo sapiensMutation(s): 2 
Gene Names: EP300P300
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens)
Explore Q09472 
Go to UniProtKB:  Q09472
PHAROS:  Q09472
GTEx:  ENSG00000100393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09472
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L3B (Subject of Investigation/LOI)
Query on A1L3B

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
4-[(2~{S})-1-[[(~{R})-[(3~{S})-7-(1-methylpyrazol-4-yl)-2,3-dihydro-1~{H}-pyrido[2,3-b][1,4]oxazin-3-yl]-phenyl-methyl]amino]propan-2-yl]benzenecarbonitrile
C28 H28 N6 O
CMLDQXRCCGCFFB-PGMDNKBISA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.194 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.4α = 90
b = 164.933β = 111.845
c = 56.588γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references