2ZNP

Human PPAR delta ligand binding domain in complex with a synthetic agonist TIPP204

PDB DOI: https://doi.org/10.2210/pdb2ZNP/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-04-30 Released: 2009-05-05
Deposition Author(s): Oyama, T., Hirakawa, Y., Nagasawa, N., Miyachi, H., Morikawa, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.288
R-Value Work: 0.230
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 64.55 kDa
Atom Count: 4,305
Modelled Residue Count: 521
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	276	Homo sapiens	Mutation(s): 0 Gene Names: PPARD, NR1C2, PPARB
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens) Explore Q03181 Go to UniProtKB: Q03181
PHAROS: Q03181 GTEx: ENSG00000112033
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03181
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K55 Query on K55 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	(2S)-2-{4-butoxy-3-[({[2-fluoro-4-(trifluoromethyl)phenyl]carbonyl}amino)methyl]benzyl}butanoic acid C₂₄ H₂₇ F₄ N O₄ AJSFKATVCYWKJN-INIZCTEOSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
B7G Query on B7G Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	heptyl beta-D-glucopyranoside C₁₃ H₂₆ O₆ NIDYWHLDTIVRJT-UJPOAAIJSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
K55	BindingDB: 2ZNP	EC50: min: 0.72, max: 0.91 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.288
R-Value Work: 0.230
R-Value Observed: 0.230
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.492	α = 90
b = 93.149	β = 97.48
c = 96.37	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-05-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-11
Changes: Database references
Version 1.3: 2016-03-02
Changes: Structure summary
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.5: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

2ZNP

Human PPAR delta ligand binding domain in complex with a synthetic agonist TIPP204

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)