9IY5 | pdb_00009iy5

WDR5 inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb9IY5/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-30 Released: 2025-08-13 
• Deposition Author(s): Wang, F., Zhou, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

WDR5 inhibitor complex structure

Wang, F., Zhou, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.16 kDa 
• Atom Count: 5,398 
• Modeled Residue Count: 610 
• Deposited Residue Count: 674 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B	334	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
PHAROS:  P61964 GTEx:  ENSG00000196363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YCP-A1EAK-A1ECH	C, D	3	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.03	α = 68.48
b = 61.447	β = 88.73
c = 64.716	γ = 67.79

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Wang, F., Zhou, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release