6D0B | pdb_00006d0b

Crystal structure of PT1614 bound to HIF2a-B*:ARNT-B* complex

• PDB DOI: https://doi.org/10.2210/pdb6D0B/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-04-10 Released: 2018-10-31 
• Deposition Author(s): Du, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PT1614 bound to HIF2a-B*:ARNT-B* complex

Du, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.18 kDa 
• Atom Count: 1,980 
• Modeled Residue Count: 219 
• Deposited Residue Count: 238 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial PAS domain-containing protein 1	A	117	Homo sapiens	Mutation(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 GTEx:  ENSG00000116016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	B	121	Homo sapiens	Mutation(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 GTEx:  ENSG00000143437

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FOV	C [auth A]	N-(3-chloro-5-fluorophenyl)-2-nitro-4-(trifluoromethanesulfonyl)aniline C13 H7 Cl F4 N2 O4 S QONODMQQXMILPX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FOV	BindingDB:  6D0B	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.841	α = 90
b = 83.254	β = 106.94
c = 41.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2026-04-15
  Changes: Data collection, Derived calculations, Structure summary