9EKP | pdb_00009ekp

Crystal structure of WDR55 in complex with XS381774

PDB DOI: https://doi.org/10.2210/pdb9EKP/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2024-12-03 Released: 2025-12-10
Deposition Author(s): Chen, U.H., Li, F., Zeng, H., Ahmad, H., Wang, X., Sun, J., Dong, A., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Peng, H., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.206 (Depositor), 0.211 (DCC)
R-Value Work:
0.156 (Depositor), 0.170 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of WDR55 in complex with XS381774

Chen, U.H., Li, F., Zeng, H., Ahmad, H., Wang, X., Sun, J., Dong, A., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Peng, H., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 69.52 kDa
Atom Count: 5,101
Modeled Residue Count: 615
Deposited Residue Count: 628
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 55	A, B	314	Homo sapiens	Mutation(s): 1 Gene Names: WDR55
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6Y2 (Homo sapiens) Explore Q9H6Y2 Go to UniProtKB: Q9H6Y2
PHAROS: Q9H6Y2 GTEx: ENSG00000120314
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H6Y2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BI5 (Subject of Investigation/LOI) Query on A1BI5 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	(7P,8S)-7-[(2S)-2-methyl-2,3-dihydro-1-benzofuran-5-yl][1,2,4]triazolo[1,5-a]pyrimidine C₁₄ H₁₂ N₄ O BPKWKBIVZRWWQO-VIFPVBQESA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [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 C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [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 H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]