9IT5 | pdb_00009it5

p300 KAT domain in complex with KB528

PDB DOI: https://doi.org/10.2210/pdb9IT5/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-07-19 Released: 2025-07-23
Deposition Author(s): Rahl, P., Gao, H., Calderon, Y., Wang, Z.-F.
Funding Organization(s): Not funded

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 1.2 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.

(2026) Cancer Res 86: 1010-1034

PubMed: 41248492 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1158/0008-5472.CAN-25-3440
Primary Citation Related Structures:
9IT5

PubMed Abstract:
The oncogenic transcription factor (TF) IRF4 is a currently undrugged universal multiple myeloma dependency. Using transcriptional regulatory network mapping, an unbiased multiomics 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 multiple myeloma-specific dependency and more closely complexed with p300 than other TFs, such as IKZF1/IKZF3. Development of optimized p300 KAT inhibitors enabled inhibition of IRF4 activity and multiple myeloma proliferation ex vivo and in vivo. p300/CBP KAT inhibition preferentially targeted multiple myeloma cells over normal cells, specifically modulating the multiple myeloma transcriptome, and the p300 KAT inhibitors more completely inhibited IRF4 activity at lower levels compared with existing p300/CREB-binding protein (CBP) bromodomain inhibitors. Furthermore, combining p300/CBP KAT inhibition and therapeutics with orthogonal mechanisms targeting transcription in multiple myeloma elicited synergistic antitumor effects. Together, these data motivate the ongoing clinical development of p300/CBP KAT inhibition in multiple myeloma. Inhibition of p300 lysine acetyltransferase activity preferentially modulates the IRF4 transcriptional regulatory network and is orthogonal to mechanisms of multiple myeloma standard-of-care treatment, supporting the translational potential of p300 inhibitors.

Organizational Affiliation

Kronos Bio, Cambridge, Massachusetts.

Macromolecule Content

Total Structure Weight: 82.09 kDa
Atom Count: 6,007
Modeled Residue Count: 660
Deposited Residue Count: 698
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300	A, B	349	Homo sapiens	Mutation(s): 2 Gene Names: EP300, P300 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09472
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L3B (Subject of Investigation/LOI) Query on A1L3B Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]