4GS9 | pdb_00004gs9

Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with an inactive benzoxadiazole antagonist

PDB DOI: https://doi.org/10.2210/pdb4GS9/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-08-27 Released: 2013-04-03
Deposition Author(s): Scheuermann, T.H., Gardner, K.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.202 (Depositor), 0.212 (DCC)
R-Value Work:
0.174 (Depositor), 0.182 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Development of Inhibitors of the PAS-B Domain of the HIF-2 alpha Transcription Factor

Rogers, J.L., Bayeh, L., Scheuermann, T.H., Longgood, J., Key, J., Naidoo, J., Melito, L., Shokri, C., Frantz, D.E., Bruick, R.K., Gardner, K.H., Macmillan, J.B., Tambar, U.K.

(2013) J Med Chem 56: 1739-1747

PubMed: 23363003 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jm301847z
Primary Citation Related Structures:
4GS9

PubMed Abstract:
Hypoxia inducible factors (HIFs) are heterodimeric transcription factors induced in a variety of pathophysiological settings, including cancer. We describe the first detailed structure-activity relationship study of small molecules designed to inhibit HIF-2α-ARNT heterodimerization by binding an internal cavity of the HIF-2α PAS-B domain. Through a series of biophysical characterizations of inhibitor-protein interactions (NMR and X-ray crystallography), we have established the structural requirements for artificial inhibitors of the HIF-2α-ARNT PAS-B interaction. These results may serve as a foundation for discovering therapeutic agents that function by a novel mode of action.

Organizational Affiliation

Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States.

Macromolecule Content

Total Structure Weight: 28.43 kDa
Atom Count: 2,074
Modeled Residue Count: 216
Deposited Residue Count: 238
Unique protein chains: 2

Macromolecules

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| 3D Structure

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: BHLHE73, EPAS1, HIF2, 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99814
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27540
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
0XB Query on 0XB Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-(3-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine C₁₂ H₇ F N₄ O₃ QMETXUTZEYHEJB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
0XB	BindingDB: 4GS9	Kd: 2200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.202 (Depositor), 0.212 (DCC)
R-Value Work: 0.174 (Depositor), 0.182 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.745	α = 90
b = 83.054	β = 105.78
c = 41.075	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Scheuermann, T.H.

Gardner, K.H.

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2018-05-30
Changes: Advisory, Data collection, Derived calculations
Version 1.2: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description