8G1Q

Co-crystal structure of Compound 1 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.73 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation.

Wurz, R.P.Rui, H.Dellamaggiore, K.Ghimire-Rijal, S.Choi, K.Smither, K.Amegadzie, A.Chen, N.Li, X.Banerjee, A.Chen, Q.Mohl, D.Vaish, A.

(2023) Nat Commun 14: 4177-4177

  • DOI: https://doi.org/10.1038/s41467-023-39904-5
  • Primary Citation of Related Structures:  
    8G1P, 8G1Q

  • PubMed Abstract: 

    Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel-Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC's architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.


  • Organizational Affiliation

    Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription activator BRG1A [auth H]124Homo sapiensMutation(s): 0 
Gene Names: SMARCA4BAF190ABRG1SNF2BSNF2L4
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51532 (Homo sapiens)
Explore P51532 
Go to UniProtKB:  P51532
PHAROS:  P51532
GTEx:  ENSG00000127616 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51532
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BB [auth A]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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CC [auth B]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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressorD [auth C]162Homo 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YHB
Query on YHB

Download Ideal Coordinates CCD File 
F [auth C]N-(2-{4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}pyridine-4-carbonyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide
C43 H50 N10 O5 S
UTVJRQFHWBOCCR-IKYVMSNGSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth H]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.73 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.163α = 90
b = 158.163β = 90
c = 44.857γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Refinement description