9BJU | pdb_00009bju

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 
    0.256 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BJU

This is version 1.1 of the entry. See complete history

Literature

Potency-Enhanced Peptidomimetic VHL Ligands with Improved Oral Bioavailability.

Wu, H.Murray, J.Ishisoko, N.Frommlet, A.Deshmukh, G.DiPasquale, A.Mulvihill, M.M.Zhang, D.Quinn, J.G.Blake, R.A.Fairbrother, W.J.Fuhrmann, J.

(2024) J Med Chem 67: 8585-8608

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02203
  • Primary Citation Related Structures: 
    9BJU, 9BOL

  • PubMed Abstract: 

    The von Hippel-Lindau (VHL) protein plays a pivotal role in regulating the hypoxic stress response and has been extensively studied and utilized in the targeted protein degradation field, particularly in the context of bivalent degraders. In this study, we present a comprehensive peptidomimetic structure-activity relationship (SAR) approach, combined with cellular NanoBRET target engagement assays to enhance the existing VHL ligands. Through systematic modifications of the molecule, we identified the 1,2,3-triazole group as an optimal substitute of the left-hand side amide bond that yields 10-fold higher binding activity. Moreover, incorporating conformationally constrained alterations on the methylthiazole benzylamine moiety led to the development of highly potent VHL ligands with picomolar binding affinity and significantly improved oral bioavailability. We anticipate that our optimized VHL ligand, GNE7599 , will serve as a valuable tool compound for investigating the VHL pathway and advancing the field of targeted protein degradation.


  • Organizational Affiliation
    • Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content 

  • Total Structure Weight: 175.29 kDa 
  • Atom Count: 11,148 
  • Modeled Residue Count: 1,361 
  • Deposited Residue Count: 1,524 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-B
A, D, G, J
104Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15370
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-C
B, E, H, K
96Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15369
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor
C, L
176Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40337
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor
F, I
176Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40337
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLEM [auth W],
N [auth X],
O [auth Y],
P [auth Z]
5synthetic constructMutation(s): 0 

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TFA

Query on TFA



Download:Ideal Coordinates CCD File
Q [auth B],
Z [auth K]
trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
R [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
AA [auth L],
W [auth H],
X [auth I]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
S [auth C],
Y [auth K]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
T [auth C],
U [auth F],
V [auth H]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
C, L
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
A1AQ4
Query on A1AQ4
M [auth W],
N [auth X],
O [auth Y],
P [auth Z]
D-PEPTIDE LINKINGC15 H15 N O2

--

HYP
Query on HYP
M [auth W],
N [auth X],
O [auth Y],
P [auth Z]
L-PEPTIDE LINKINGC5 H9 N O3PRO
TBG
Query on TBG
M [auth W],
N [auth X],
O [auth Y],
P [auth Z]
L-PEPTIDE LINKINGC6 H13 N O2VAL

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free:  0.256 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.297α = 90
b = 93.297β = 90
c = 362.757γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary