7F80 | pdb_00007f80

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), 0.302 (DCC)
R-Value Work:
0.204 (Depositor), 0.213 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 509
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03181
Sequence Annotations Expand
Reference Sequence

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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.300 (Depositor), 0.302 (DCC)
R-Value Work: 0.204 (Depositor), 0.213 (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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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.