8ZCI | pdb_00008zci

X-ray structure of the human heart fatty acid-binding protein complexed with R-Ibuprofen

PDB DOI: https://doi.org/10.2210/pdb8ZCI/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-29 Released: 2025-04-30
Deposition Author(s): Sugiyama, S., Tanaka, J., Matsuoka, S., Murata, M.
Funding Organization(s): Japan Science and Technology, Other private, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.166 (Depositor), 0.168 (DCC)
R-Value Work:
0.132 (Depositor), 0.134 (DCC)
R-Value Observed:
0.134 (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

X-ray structure of the human heart fatty acid-binding protein complexed with R-Ibuprofen

Sugiyama, S., Tanaka, J., Matsuoka, S., Murata, M.

To be published.

Macromolecule Content

Total Structure Weight: 15.69 kDa
Atom Count: 1,403
Modelled Residue Count: 133
Deposited Residue Count: 133
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, heart	A	133	Homo sapiens	Mutation(s): 0 Gene Names: FABP3, FABP11, MDGI
UniProt & NIH Common Fund Data Resources
Find proteins for P05413 (Homo sapiens) Explore P05413 Go to UniProtKB: P05413
PHAROS: P05413 GTEx: ENSG00000121769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05413
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IZP (Subject of Investigation/LOI) Query on IZP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid C₁₃ H₁₈ O₂ HEFNNWSXXWATRW-SNVBAGLBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.166 (Depositor), 0.168 (DCC)
R-Value Work: 0.132 (Depositor), 0.134 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.201	α = 90
b = 107.868	β = 90
c = 48.146	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER1005
Japan Science and Technology	Japan	JPMJTM19DC
Other private	Japan	09-003-005
Japan Society for the Promotion of Science (JSPS)	Japan	19K06588