7RCU

Synthetic Max homodimer mimic in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains.

Speltz, T.E.Qiao, Z.Swenson, C.S.Shangguan, X.Coukos, J.S.Lee, C.W.Thomas, D.M.Santana, J.Fanning, S.W.Greene, G.L.Moellering, R.E.

(2023) Nat Biotechnol 41: 541-551

  • DOI: https://doi.org/10.1038/s41587-022-01504-x
  • Primary Citation of Related Structures:  
    7RCU

  • PubMed Abstract: 

    Despite unequivocal roles in disease, transcription factors (TFs) remain largely untapped as pharmacologic targets due to the challenges in targeting protein-protein and protein-DNA interactions. Here we report a chemical strategy to generate modular synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX. Our synthetic approach yields chemically stabilized tertiary domain mimetics that cooperatively bind the MYC/MAX consensus E-box motif with nanomolar affinity, exhibit specificity that is equivalent to or beyond that of full-length TFs and directly compete with MYC/MAX protein for DNA binding. A lead STR directly inhibits MYC binding in cells, downregulates MYC-dependent expression programs at the proteome level and inhibits MYC-dependent cell proliferation. Co-crystallization and structure determination of a STR:E-box DNA complex confirms retention of DNA recognition in a near identical manner as full-length bHLH TFs. We additionally demonstrate structure-blind design of STRs derived from alternative bHLH-TFs, confirming that STRs can be used to develop highly specific mimetics of TFs targeting other gene regulatory elements.


  • Organizational Affiliation

    Department of Chemistry, University of Chicago, Chicago, IL, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein max28Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61244 (Homo sapiens)
Explore P61244 
Go to UniProtKB:  P61244
PHAROS:  P61244
GTEx:  ENSG00000125952 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61244
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein max20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61244 (Homo sapiens)
Explore P61244 
Go to UniProtKB:  P61244
PHAROS:  P61244
GTEx:  ENSG00000125952 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61244
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*A*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*A)-3')17synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*G*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*A)-3')F [auth D]16synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DA
Query on DA

Download Ideal Coordinates CCD File 
BA [auth D]2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
V7J (Subject of Investigation/LOI)
Query on V7J

Download Ideal Coordinates CCD File 
AA [auth Q]
CA [auth V]
EA [auth F]
FA [auth J]
GA [auth U]
AA [auth Q],
CA [auth V],
EA [auth F],
FA [auth J],
GA [auth U],
Y [auth S]
2-(2,5-dioxopyrrolidin-1-yl)acetamide
C6 H8 N2 O3
RLSJGKULBJWLEW-UHFFFAOYSA-N
ACM
Query on ACM

Download Ideal Coordinates CCD File 
DA [auth V],
Z [auth S]
ACETAMIDE
C2 H5 N O
DLFVBJFMPXGRIB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.666α = 90.05
b = 46.266β = 90.05
c = 166.017γ = 90.02
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-05-03
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-03-13
    Changes: Source and taxonomy