9OGW: E3 ubiquitin-protein ligase CBL-C

Name: PDB 9OGW: Identification of ligands for E3 ligases using fragment-based methods
Published: 2025-10-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Identification of ligands for E3 ligases using fragment-based methods. Determined by X-ray diffraction at 1.8 Å resolution. Released 22 Oct 2025.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,547
Mol. weight: 35.7 kDa
Ligands: A1CA8
Released: 22 Oct 2025

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

Secondary structure: helices and β-sheets

9OGW contains 15 α-helices and 7 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: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	44-65	22
α-helix	76-97	22
α-helix	116-138	23
α-helix	140-142	3
α-helix	154-163	10
β-strand	169-171	3	1
α-helix	172-180	9
α-helix	189-198	10
β-strand	205-207	3	1
α-helix	208-217	10
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-233	5
β-strand	238	1	2
α-helix	244-252	9
β-strand	260-265	6	2
β-strand	273-278	6	2
β-strand	284-287	4	2
α-helix	294-303	10
β-strand	309-310	2	2
α-helix	315-318	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase CBL-C	A	protein	318	Homo sapiens	Q9ULV8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9OGW_1 E3 ubiquitin-protein ligase CBL-C (chains A)
VAPWGRQWEEARALGRAVRMLQRLEEQCVDPRLSVSPPSLRDLLPRTAQLLREVAHSRRA
AGGGGPGGPGGSGDFLLIYLANLEAKSRQVAALLPPRGRRSANDELFRAGSRLRRQLAKL
AIIFSHMHAELHALFPGGKYCGHMYQLTKAPAHTFWRESCGARCVLPWAEFESLLGTCHP
VEPGCTALALRTTIDLTCSGHVSIFEFDVFTRLFQPWPTLLKNWQLLAVNHPGYMAFLTY
DEVQERLQACRDKPGSYIFRPSCTRLGQWAIGYVSSDGSILQTIPANKPLSQVLLEGQKD
GFYLYPDGKTHNPDLTEL

Ligands and cofactors

ID	Name	Formula	Copies
A1CA8	2-{[(thiophen-3-yl)methyl]amino}benzoic acid	C12 H11 N O2 S	1

Primary citation

Identification of ligands for E3 ligases with restricted expression using fragment-based methods. Waterson, A.G., Lehmann, B.D., Lu, Z. et al. RSC Chem Biol (2025) 6:1797-1808. DOI 10.1039/d5cb00198f · PubMed

Other PDB entries of the same protein (UniProt Q9ULV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VRP 1.52 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with…
3VRN 1.64 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c
3VRO 1.8 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with…
3VRR 2.0 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c (PL mutant) in complex…
3VRQ 2.39 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c (PL mutant)
3OP0 2.52 Å, Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide

Browse structure collections

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