6DFN

Crystal structure of estrogen receptor alpha in complex with receptor degrader 16aa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unexpected equivalent potency of a constrained chromene enantiomeric pair rationalized by co-crystal structures in complex with estrogen receptor alpha.

Zhang, B.Kiefer, J.R.Blake, R.A.Chang, J.H.Hartman, S.Ingalla, E.R.Kleinheinz, T.Mody, V.Nannini, M.Ortwine, D.F.Ran, Y.Sambrone, A.Sampath, D.Vinogradova, M.Zhong, Y.Nwachukwu, J.C.Nettles, K.W.Lai, T.Liao, J.Zheng, X.Chen, H.Wang, X.Liang, J.

(2019) Bioorg. Med. Chem. Lett. 29: 905-911


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A, B, C, D
280Homo sapiensMutation(s): 0 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G9J
Query on G9J

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A, B, C, D
(2S)-3-(3-hydroxyphenyl)-2-(4-iodophenyl)-4-methyl-2H-1-benzopyran-6-ol
C22 H17 I O3
RWKXMXMLZHFKIZ-QFIPXVFZSA-N
 Ligand Interaction
GOL
Query on GOL

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B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
G91
Query on G91

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B, D
(8S)-8-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-1,8-dihydro-2H-[1]benzopyrano[4,3-d][1]benzoxepine-5,11-diol
C29 H28 F N O5
OXWBLBDJUUJFFV-LJAQVGFWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.089α = 86.05
b = 59.134β = 74.92
c = 94.180γ = 63.34
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references