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)

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 9IY5

This is version 1.0 of the entry. See complete history.

Literature

WDR5 inhibitor complex structure

Wang, F., Zhou, C.

To be published.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61964
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

Small Molecules

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1EAK Query on A1EAK	C, D	D-PEPTIDE LINKING	C₇ H₁₃ N O₂		--
A1ECH Query on A1ECH	C, D	D-PEPTIDE LINKING	C₁₂ H₁₈ N₂ O		--
YCP Query on YCP	C, D	L-PEPTIDE LINKING	C₆ H₁₁ N O₂		--

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.