9OIO | pdb_00009oio

The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragments 9 and 14

PDB DOI: https://doi.org/10.2210/pdb9OIO/pdb

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

Deposited: 2025-05-06 Released: 2025-07-09
Deposition Author(s): Amporndanai, K., Katinas, J.M., Chopra, A., Fesik, S.W.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

NMR-Based Fragment Screen of the von Hippel-Lindau Elongin C&B Complex.

Amporndanai, K., Katinas, J.M., Chopra, A., Kayode, O., Vadukoot, A.K., Waterson, A.G., Fesik, S.W.

(2025) ACS Med Chem Lett 16: 1648-1654

PubMed: 40832550 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.5c00316
Primary Citation Related Structures:
9OIM, 9OIN, 9OIO, 9OIQ

PubMed Abstract:
von Hippel-Lindau (VHL) is an E3 ligase that has been widely exploited for the development of PROTACs to induce degradation of disease-associated target proteins. Nearly all VHL-recruiting PROTACs contain a hydroxyproline moiety based on the endogenous peptide substrate that occupies the HIF1α-binding site of VHL. However, the development of orally bioavailable PROTACs with hydroxyproline-based VHL ligands remains a significant hurdle, due to both the hydroxyproline and the peptidic nature of the VHL ligand. Here, we describe an NMR-based fragment screen against the VHL-Elongin C-Elongin B (VCB) complex. Several hits were shown by X-ray crystallography to bind to the HIF1α active site in VHL of the VCB complex, which opens the possibility for the discovery of new nonhydroxyproline-based VHL ligands for use in VHL-recruiting PROTACs.

Organizational Affiliation

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.

Macromolecule Content

Total Structure Weight: 176.15 kDa
Atom Count: 10,766
Modeled Residue Count: 1,322
Deposited Residue Count: 1,528
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A, D, G, J	104	Homo sapiens	Mutation(s): 0 Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370
PHAROS: Q15370 GTEx: ENSG00000103363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B, E, H, K	98	Homo sapiens	Mutation(s): 0 Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369
PHAROS: Q15369 GTEx: ENSG00000154582
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	C, F, L	180	Homo sapiens	Mutation(s): 0 Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337
PHAROS: P40337 GTEx: ENSG00000134086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	I	180	Homo sapiens	Mutation(s): 0 Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337
PHAROS: P40337 GTEx: ENSG00000134086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CBL (Subject of Investigation/LOI) Query on A1CBL Download:Ideal Coordinates CCD File SDF format, chain W [auth L] SDF format, chain P [auth F] SDF format, chain M [auth C] MOL2 format, chain W [auth L] MOL2 format, chain P [auth F] MOL2 format, chain M [auth C] mmCIF format, chain W [auth L] mmCIF format, chain P [auth F] mmCIF format, chain M [auth C]	M [auth C], P [auth F], W [auth L]	1-[(2-fluorophenyl)methyl]-4-(propan-2-yl)piperazine C₁₄ H₂₁ F N₂ SPOGRIJAQWZVBH-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain P [auth F] Focus chain W [auth L] Interactions & Density Focus chain M [auth C] Focus chain P [auth F] Focus chain W [auth L]
A1CBK (Subject of Investigation/LOI) Query on A1CBK Download:Ideal Coordinates CCD File SDF format, chain V [auth K] SDF format, chain S [auth H] SDF format, chain O [auth E] MOL2 format, chain V [auth K] MOL2 format, chain S [auth H] MOL2 format, chain O [auth E] mmCIF format, chain V [auth K] mmCIF format, chain S [auth H] mmCIF format, chain O [auth E]	O [auth E], S [auth H], V [auth K]	1-[6-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone C₁₀ H₁₀ N₂ O₃ RLXSSISTKOLICZ-UHFFFAOYSA-N		Interactions Focus chain O [auth E] Focus chain S [auth H] Focus chain V [auth K] Interactions & Density Focus chain O [auth E] Focus chain S [auth H] Focus chain V [auth K]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain U [auth I] SDF format, chain T [auth H] SDF format, chain R [auth F] SDF format, chain Q [auth F] SDF format, chain N [auth C] MOL2 format, chain X [auth L] MOL2 format, chain U [auth I] MOL2 format, chain T [auth H] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain N [auth C] mmCIF format, chain X [auth L] mmCIF format, chain U [auth I] mmCIF format, chain T [auth H] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain N [auth C]	N [auth C] Q [auth F] R [auth F] T [auth H] U [auth I] N [auth C], Q [auth F], R [auth F], T [auth H], U [auth I], X [auth L]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain Q [auth F] Focus chain R [auth F] Focus chain T [auth H] Focus chain U [auth I] Focus chain X [auth L] Interactions & Density Focus chain N [auth C] Focus chain Q [auth F] Focus chain R [auth F] Focus chain T [auth H] Focus chain U [auth I] Focus chain X [auth L]