6D09

Crystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Literature

Crystal structure of PT1940 bound to HIF2a-B*:ARNT-B* complex

Du, X.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endothelial PAS domain-containing protein 1A117Homo sapiensMutation(s): 1 
Gene Names: EPAS1, BHLHE73, HIF2A, MOP2, PASD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens)
Explore Q99814 
Go to UniProtKB:  Q99814
PHAROS:  Q99814
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99814
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocatorB121Homo sapiensMutation(s): 1 
Gene Names: ARNT, BHLHE2
UniProt & NIH Common Fund Data Resources
Find proteins for P27540 (Homo sapiens)
Explore P27540 
Go to UniProtKB:  P27540
PHAROS:  P27540
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27540
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FOJ
Query on FOJ
Download Ideal Coordinates CCD File 
C [auth A]3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile
C16 H8 F5 N O4 S
HZDKYXAZAPXCKQ-CQSZACIVSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FOJ BindingDB:  6D09 IC50: min: 5, max: 14 (nM) from 2 assay(s)
EC50: min: 10, max: 145 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.216α = 90
b = 83.832β = 106.25
c = 41.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2018-10-31 
    • Deposition Author(s): Du, X.

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release