6OCJ

Crystal Structure of Equine Serum Albumin in Complex with Suprofen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Currently 6OCJ does not have a validation slider image.


This is version 1.3 of the entry. See complete history


Literature

Structural investigations of stereoselective profen binding by equine and leporine serum albumins.

Zielinski, K.Sekula, B.Bujacz, A.Szymczak, I.

(2020) Chirality 32: 334-344

  • DOI: https://doi.org/10.1002/chir.23162
  • Primary Citation of Related Structures:  
    6OCI, 6OCJ, 6OCK, 6OCL

  • PubMed Abstract: 

    Serum albumin, the most abundant transport protein of mammalian blood, interacts with various nonsteroidal anti-inflammatory drugs (NSAIDs) affecting their disposition, metabolism, and excretion. A big group of chiral NSAIDs transported by albumin, profens, is created by derivatives of 2-arylpropionic acid. The chiral center in the structures of profens is adjacent to the carboxylate moiety and often determines different pharmacological properties of profen enantiomers. This study describes crystal structures of two albumins, isolated from equine and leporine serum, in complexes with three profens: ibuprofen, ketoprofen, and suprofen. Based on three-dimensional structures, the stereoselectivity of albumin is discussed and referred to the previously published albumin complexes with drugs. Drug Site 2 (DS2) of albumin, the bulky hydrophobic pocket of subdomain IIIA with a patch of polar residues, preferentially binds (S)-enantiomers of all investigated profens. Almost identical binding mode of all these drugs clearly indicates the stereoselectivity of DS2 towards (S)-profens in different albumin species. Also, the affinity studies show that DS2 is the major site that presents high affinity towards investigated drugs. Additionally, crystallographic data reveal the secondary binding sites of ketoprofen in leporine serum albumin and ibuprofen in equine serum albumin, both overlapping with previously identified naproxen binding sites: the cleft formed between subdomains IIIA and IIIB close to the fatty acid binding site 5 and the niche created between subdomains IIA and IIIA, called fatty acid site 6.


  • Organizational Affiliation

    Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serum albumin583Equus caballusMutation(s): 0 
UniProt
Find proteins for P35747 (Equus caballus)
Explore P35747 
Go to UniProtKB:  P35747
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35747
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M5A
Query on M5A

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-[4-(thiophene-2-carbonyl)phenyl]propanoic acid
C14 H12 O3 S
MDKGKXOCJGEUJW-VIFPVBQESA-N
SIN
Query on SIN

Download Ideal Coordinates CCD File 
D [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
C [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.261α = 90
b = 95.261β = 90
c = 144.533γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
STARANISOdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Currently 6OCJ does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary