7F80

Co-crystal structure of Inhibitor compound MA-211 in complex with human PPARdelta LBD

PDB DOI: https://doi.org/10.2210/pdb7F80/pdb

Classification: PROTEIN BINDING/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2021-06-30 Released: 2022-07-06
Deposition Author(s): Lakshminarasimhan, A., Rani, S.T., Senaiar, R.S., Krishnamurthy, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.300 (Depositor), 0.300 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Co-crystal structure of Inhibitor compound in complex with human PPARdelta LBD

Lakshminarasimhan, A., Rani, S.T., Senaiar, R.S., Krishnamurthy, N.

To be published.

Macromolecule Content

Total Structure Weight: 63.78 kDa
Atom Count: 4,176
Modelled Residue Count: 509
Deposited Residue Count: 550
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	275	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 LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1KF (Subject of Investigation/LOI) Query on 1KF Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(3R)-3-methyl-6-[2-[[5-methyl-2-[4-(trifluoromethyl)phenyl]imidazol-1-yl]methyl]phenoxy]hexanoic acid C₂₅ H₂₇ F₃ N₂ O₃ FMOPHFSPINWSOV-QGZVFWFLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
1KF	BindingDB: 7F80	EC50: 0.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.300 (Depositor), 0.300 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.687	α = 90
b = 74.991	β = 97.89
c = 96.341	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Lakshminarasimhan, A.

Krishnamurthy, N.

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.