7S4E

Crystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry.

Dixon, T.MacPherson, D.Mostofian, B.Dauzhenka, T.Lotz, S.McGee, D.Shechter, S.Shrestha, U.R.Wiewiora, R.McDargh, Z.A.Pei, F.Pal, R.Ribeiro, J.V.Wilkerson, T.Sachdeva, V.Gao, N.Jain, S.Sparks, S.Li, Y.Vinitsky, A.Zhang, X.Razavi, A.M.Kolossvary, I.Imbriglio, J.Evdokimov, A.Bergeron, L.Zhou, W.Adhikari, J.Ruprecht, B.Dickson, A.Xu, H.Sherman, W.Izaguirre, J.A.

(2022) Nat Commun 13: 5884-5884

  • DOI: https://doi.org/10.1038/s41467-022-33575-4
  • Primary Citation of Related Structures:  
    7S4E

  • PubMed Abstract: 

    Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.


  • Organizational Affiliation

    Roivant Discovery, New York City, NY, 10036, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Short of Probable global transcription activator SNF2L2
A, E
125Homo sapiensMutation(s): 0 
Gene Names: SMARCA2BAF190BBRMSNF2ASNF2L2
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens)
Explore P51531 
Go to UniProtKB:  P51531
PHAROS:  P51531
GTEx:  ENSG00000080503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51531
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor
B, F
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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C
C, G
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  
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UniProt GroupQ15369
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B
D, H
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 
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UniProt GroupQ15370
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
87A (Subject of Investigation/LOI)
Query on 87A

Download Ideal Coordinates CCD File 
T [auth B],
Z [auth F]
N-(1-fluorocyclopropane-1-carbonyl)-3-methyl-L-valyl-(4R)-N-{[2-{2-[4-({4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}methyl)phenoxy]ethoxy}-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-4-hydroxy-L-prolinamide
C49 H58 F N9 O7 S
IVARZBJJMMUJHI-SQKKEFIPSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
N [auth B],
P [auth B],
W [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth G]
I [auth A]
J [auth A]
K [auth A]
M [auth B]
AA [auth G],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
O [auth B],
U [auth D],
V [auth D],
X [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth A],
Q [auth B],
R [auth B],
S [auth B],
Y [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.14α = 90
b = 116.57β = 90
c = 122.32γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description