9PY8 | pdb_00009py8

Menin mutant - G331R in complex with Ziftomenib

• PDB DOI: https://doi.org/10.2210/pdb9PY8/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-08-07 Released: 2026-10-28 
• Deposition Author(s): Clegg, B.D., Cierpicki, T., Grembecka, J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.144 (DCC) 

Starting Model: experimental

Literature

Menin mutant - G331R in complex with Ziftomenib

Clegg, B.D., Cierpicki, T., Grembecka, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 55.77 kDa 
• Atom Count: 4,665 
• Modeled Residue Count: 469 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menin	A	489	Homo sapiens	Mutation(s): 1  Gene Names: MEN1, SCG2
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens) Explore O00255  Go to UniProtKB:  O00255
PHAROS:  O00255 GTEx:  ENSG00000133895

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K5O (Subject of Investigation/LOI)	B [auth A]	Ziftomenib C33 H42 F3 N9 O2 S2 BGGALFIXXQOTPY-NRFANRHFSA-N
PEG	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.144 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.083	α = 90
b = 80.126	β = 90
c = 124.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Clegg, B.D., Cierpicki, T., Grembecka, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	272561

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release