5WGQ

Estrogen Receptor Alpha Ligand Binding Domain in Complex with Estradiol and SRC2-BCP1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

A "cross-stitched" peptide with improved helicity and proteolytic stability.

Speltz, T.E., Mayne, C.G., Fanning, S.W., Siddiqui, Z., Tajkhorshid, E., Greene, G.L., Moore, T.W.

(2018) Org Biomol Chem 16: 3702-3706

  • DOI: https://doi.org/10.1039/c8ob00790j
  • Primary Citation of Related Structures:  
    5WGD, 5WGQ

  • PubMed Abstract: 

    A new computational approach to obtain quantitative energy profiles for helix folding was used in the design of orthogonal hydrocarbon and lactam bicyclic peptides. The proteolytically stable, "cross-stitched" peptide SRC2-BCP1 shows nanomolar affinity for estrogen receptor α and X-ray crystallography confirms a helical binding pose.

    • Organizational Affiliation: 

    Department of Medicinal Chemistry and Pharmacognosy and UI Cancer Center, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. [email protected].


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
261Homo sapiensMutation(s): 1 
Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SRC2-BCP1C [auth E],
D [auth F]		13synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MK8
Query on MK8		C [auth E],
D [auth F]		L-PEPTIDE LINKINGC7 H15 N O2LEU
Binding Affinity Annotations 
IDSourceBinding Affinity
EST BindingDB:  5WGQ Ki: min: 0.11, max: 100 (nM) from 14 assay(s)
Kd: min: 0.2, max: 3.5 (nM) from 3 assay(s)
IC50: min: 1.00e-2, max: 46 (nM) from 50 assay(s)
EC50: min: 4.00e-3, max: 10 (nM) from 53 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.038α = 90
b = 84.044β = 111.25
c = 58.209γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Structure summary
  • Version 1.2: 2020-02-26
    Changes: Advisory, Derived calculations
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-10-30
    Changes: Structure summary