9WGU | pdb_00009wgu

Crystal structure of Cbl-b bound to compound

PDB DOI: https://doi.org/10.2210/pdb9WGU/pdb

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

Deposited: 2025-08-25 Released: 2026-09-02
Deposition Author(s): Fan, Y., Ding, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.226 (Depositor), 0.233 (DCC)
R-Value Work:
0.174 (Depositor), 0.183 (DCC)

Starting Model: in silico
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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 Cbl-b bound to compound

Fan, Y., Ding, X.

To be published.

Macromolecule Content

Total Structure Weight: 92.39 kDa
Atom Count: 7,019
Modeled Residue Count: 766
Deposited Residue Count: 776
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 [auth AAA], B [auth BBB]	388	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EWZ (Subject of Investigation/LOI) Query on A1EWZ Download:Ideal Coordinates CCD File SDF format, chain M [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain M [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain M [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], M [auth BBB]	2-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-7-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-3,4-dihydroisoquinolin-1-one C₃₁ H₃₆ F₃ N₅ O PQPUBPMJVGYMCT-FNFPNEPISA-N		Interactions Focus chain C [auth AAA] Focus chain M [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain M [auth BBB]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth BBB] SDF format, chain N [auth BBB] SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain O [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA], E [auth AAA], N [auth BBB], O [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain N [auth BBB] Focus chain O [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain N [auth BBB] Focus chain O [auth BBB]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth BBB] SDF format, chain V [auth BBB] SDF format, chain U [auth BBB] SDF format, chain T [auth BBB] SDF format, chain S [auth BBB] SDF format, chain R [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain L [auth AAA] SDF format, chain K [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] MOL2 format, chain W [auth BBB] MOL2 format, chain V [auth BBB] MOL2 format, chain U [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain W [auth BBB] mmCIF format, chain V [auth BBB] mmCIF format, chain U [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain R [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA] H [auth AAA] I [auth AAA] J [auth AAA] K [auth AAA] G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], Q [auth BBB], R [auth BBB], S [auth BBB], T [auth BBB], U [auth BBB], V [auth BBB], W [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Focus chain V [auth BBB] Focus chain W [auth BBB] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Focus chain V [auth BBB] Focus chain W [auth BBB]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth BBB] SDF format, chain F [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain F [auth AAA] mmCIF format, chain P [auth BBB] mmCIF format, chain F [auth AAA]	F [auth AAA], P [auth BBB]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain P [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain P [auth BBB]