5ZWH | pdb_00005zwh

Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having an ene-ynone group via conjugate addition reaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.279 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.235 (Depositor) 
  • R-Value Observed: 
    0.237 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZWH

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands

Yoshizawa, M.Itoh, T.Hori, T.Kato, A.Anami, Y.Yoshimoto, N.Yamamoto, K.

(2018) J Med Chem 61: 6339-6349

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00774
  • Primary Citation Related Structures: 
    5ZWE, 5ZWF, 5ZWH, 5ZWI

  • PubMed Abstract: 

    We designed and synthesized vitamin D analogues with an electrophile as covalent modifiers for the vitamin D receptor (VDR). Novel vitamin D analogues 1-4 have an electrophilic enone group at the side chain for conjugate addition to His301 or His393 in the VDR. All compounds showed specific VDR-binding potency and agonistic activity. Covalent bond formations of 1-4 with the ligand-binding domain (LBD) of VDR were evaluated by electrospray ionization mass spectrometry. All compounds were shown to covalently bind to the VDR-LBD, and the abundance of VDR-LBD corresponding conjugate adducts of 1-4 increased with incubation time. Enone compounds 1 and 2 showed higher reactivity than the ene-ynone 3 and dienone 4 compounds. Furthermore, we successfully obtained cocrystals of VDR-LBD with analogues 1-4. X-ray crystallographic analysis showed a covalent bond with His301 in VDR-LBD. We successfully synthesized vitamin D analogues that form a covalent bond with VDR-LBD.


  • Organizational Affiliation
    • Laboratory of Drug Design and Medicinal Chemistry , Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen , Machida, Tokyo 194-8543 , Japan.

Macromolecule Content 

  • Total Structure Weight: 32.99 kDa 
  • Atom Count: 2,001 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 284 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vitamin D3 receptor271Rattus norvegicusMutation(s): 0 
Gene Names: VdrNr1i1
UniProt
Find proteins for P13053 (Rattus norvegicus)
Explore P13053 
Go to UniProtKB:  P13053
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13053
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
13-meric peptide from DRIP205 NR2 BOX peptideB [auth C]13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens)
Explore Q15648 
Go to UniProtKB:  Q15648
PHAROS:  Q15648
GTEx:  ENSG00000125686 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15648
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9KX

Query on 9KX



Download:Ideal Coordinates CCD File
C [auth A](2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one
C27 H38 O3
NXEUFUPQFMVYDT-SVJWBRFGSA-N
9N9

Query on 9N9



Download:Ideal Coordinates CCD File
D [auth A](E,2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-6-en-4-yn-3-one
C27 H36 O3
LQJPGHNFADIMOG-QHQWRQFTSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.279 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.235 (Depositor) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.3α = 90
b = 42.52β = 95.72
c = 41.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary