9XZD: E3 ubiquitin-protein ligase CBL-B

Name: PDB 9XZD: E3 ubiquitin-protein ligase CBL-B in complex with compound 8
Published: 2026-09-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

E3 ubiquitin-protein ligase CBL-B in complex with compound 8. Determined by X-ray diffraction at 1.65 Å resolution. Released 2 Sept 2026.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,288
Mol. weight: 46.42 kDa
Ligands: CA, ZN, XLH
Released: 2 Sept 2026

Explore 9XZD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XZD contains 21 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	43-60	18
α-helix	74-91	18
α-helix	99-102	4
α-helix	105-128	24
α-helix	129-133	5
α-helix	138-160	23
α-helix	162-164	3
α-helix	168-170	3
α-helix	176-186	11
β-strand	191-193	3	1
α-helix	194-204	11
α-helix	210-220	11
β-strand	227-229	3	1
α-helix	230-239	10
α-helix	243-245	3
α-helix	246-250	5
α-helix	251-255	5
β-strand	260-263	4	2
α-helix	266-274	9
β-strand	282-287	6	2
β-strand	295-300	6	2
β-strand	306-309	4	2
α-helix	316-325	10
β-strand	331-332	2	2
α-helix	342-345	4
α-helix	357-364	8
β-strand	372	1	3
β-strand	380	1	3
β-strand	383-386	4	4
β-strand	390-392	3	4
α-helix	394-402	9
α-helix	413-415	3
β-strand	417-420	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase CBL-B	A	protein	392	Homo sapiens	Q13191 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9XZD_1 E3 ubiquitin-protein ligase CBL-B (chains A)
GSQAAADRRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYDDN
QKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEEQSQDRRNLTKLSLIFSHMLA
EIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMA
LKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQK
YSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGR
SYNPDLTGLCEPTPHDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTS
CLTAWQESDGQGCPFCRCEIKGTEPIIVDPFD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
ZN	Zinc ion	Zn	2
XLH	N-(3-{(1S)-1-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]ethyl}phenyl)-6-(trifluo…	C18 H16 F3 N5 O S	1

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Discovery and characterization of Cbl-b intra-molecular inhibitory glues with biological activity. Gajewski, S. To be published.

Other PDB entries of the same protein (UniProt Q13191 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QTG 1.42 Å, Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 9)
8QTJ 1.52 Å, Crystal structure of Cbl-b in complex with an allosteric inhibitor (compound 30)
2OOA 1.56 Å, crystal structure of the UBA domain from Cbl-b ubiquitin ligase
9FQJ 1.56 Å, E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12)
9I0B 1.66 Å, E3 ubiquitin ligase CBL-B in complex with inhibitor
2J6F 1.7 Å, N-terminal SH3 domain of cms (CD2AP human homolog) bound to cbl-B peptide
9XZB 1.75 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 2
8VW5 1.76 Å, Crystal structure of Cbl-b TKB bound to compound 2
10ZJ 1.77 Å, Structure of Cbl-B bound to compound 8
9FQH 1.79 Å, E3 ligase Cbl-b in complex with a triazolone core inhibitor (compound 1)
9XZC 1.8 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 6
8GCY 1.81 Å, Co-crystal structure of CBL-B in complex with N-Aryl isoindolin-1-one inhibitor

Browse structure collections

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