8YWV | pdb_00008ywv

Human PPAR alpha ligand binding domain in complex with a 1H-pyrazolo[3,4-b]pyridine-derived compound

PDB DOI: https://doi.org/10.2210/pdb8YWV/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-01 Released: 2025-04-09
Deposition Author(s): Tachibana, K., Morie, T., Fukuda, S., Yuzuriha, T., Ishimoto, K., Nunomura, K., Lin, B., Miyachi, H., Oki, H., Kawahara, K., Meguro, K., Nakagawa, S., Tsujikawa, K., Akai, S., Doi, T., Yoshida, T.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural evolution of 1H-pyrazolo[3,4-b]pyridine-derived PPARalpha activators as leads for nonalcoholic steatohepatitis

Tachibana, K., Morie, T., Fukuda, S., Yuzuriha, T., Ishimoto, K., Nunomura, K., Lin, B., Miyachi, H., Oki, H., Kawahara, K., Meguro, K., Nakagawa, S., Tsujikawa, K., Akai, S., Doi, T., Yoshida, T.

To be published.

Macromolecule Content

Total Structure Weight: 33.6 kDa
Atom Count: 2,258
Modeled Residue Count: 269
Deposited Residue Count: 294
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor alpha	A	272	Homo sapiens	Mutation(s): 0 Gene Names: PPARA, NR1C1, PPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens) Explore Q07869 Go to UniProtKB: Q07869
PHAROS: Q07869 GTEx: ENSG00000186951
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07869
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B	22	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2 Go to UniProtKB: Q9UBK2
PHAROS: Q9UBK2 GTEx: ENSG00000109819
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L0A (Subject of Investigation/LOI) Query on A1L0A 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]	1-(4-fluorophenyl)-6-[4-(2-methylpropoxycarbonyl)piperazin-1-yl]-3-pentan-3-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid C₂₇ H₃₄ F N₅ O₄ HISOUHMSGUISKF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.025	α = 90
b = 61.493	β = 90
c = 97.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121054
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121052
Japan Society for the Promotion of Science (JSPS)	Japan	15H02896
Japan Society for the Promotion of Science (JSPS)	Japan	16K13044
Japan Society for the Promotion of Science (JSPS)	Japan	18H03190
Japan Society for the Promotion of Science (JSPS)	Japan	21H03354