9WDH | pdb_00009wdh

Crystal Structure of CBL-B in Complex with a Potent Inhibitor Demonstrating In Vivo Efficacy

PDB DOI: https://doi.org/10.2210/pdb9WDH/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-19 Released: 2026-08-26
Deposition Author(s): Sun, G., Wang, H., Liu, C., Zhang, B., Wang, Y., Xin, B., Jiang, D., Wang, H., Huang, B.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.309 (Depositor), 0.308 (DCC)
R-Value Work:
0.285 (Depositor), 0.283 (DCC)
R-Value Observed:
0.287 (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

A Unified 3D Molecular Generation Platform for Novel Scaffold Discovery and Hit-to-Lead Optimization Leading to Cbl-b Inhibitor Discovery with In Vivo Efficacy

Wang, H., Sun, G., Zhang, B., Wang, Y., Xin, B., Yang, M., Liu, C., Zhou, F., Liu, Z., Jiang, D., Wang, H., Zhou, W., Huang, B.

To be published.

Macromolecule Content

Total Structure Weight: 92.71 kDa
Atom Count: 6,483
Modeled Residue Count: 762
Deposited Residue Count: 788
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL-B	A, B	394	Homo sapiens	Mutation(s): 0 Gene Names: CBLB, RNF56, Nbla00127 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q13191 (Homo sapiens) Explore Q13191 Go to UniProtKB: Q13191
PHAROS: Q13191 GTEx: ENSG00000114423
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EVY (Subject of Investigation/LOI) Query on A1EVY 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]	5-fluoranyl-3-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-8-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-1~{H}-quinolin-2-one C₃₀ H₃₄ F N₅ O GPLWCDZHXDFSFU-PRWCENSBSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
ZN Query on ZN 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] SDF format, chain D [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] MOL2 format, chain D [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] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]