6U4R | pdb_00006u4r

Crystal structure of Equine Serum Albumin complex with ketoprofen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.233 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma.

Czub, M.P.Handing, K.B.Venkataramany, B.S.Cooper, D.R.Shabalin, I.G.Minor, W.

(2020) J Med Chem 63: 6847-6862

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00225
  • Primary Citation Related Structures: 
    5V0V, 6CI6, 6U4R, 6U4X, 6U5A

  • PubMed Abstract: 

    Every day, hundreds of millions of people worldwide take nonsteroidal anti-inflammatory drugs (NSAIDs), often in conjunction with multiple other medications. In the bloodstream, NSAIDs are mostly bound to serum albumin (SA). We report the crystal structures of equine serum albumin complexed with four NSAIDs (ibuprofen, ketoprofen, etodolac, and nabumetone) and the active metabolite of nabumetone (6-methoxy-2-naphthylacetic acid, 6-MNA). These compounds bind to seven drug-binding sites on SA. These sites are generally well-conserved between equine and human SAs, but ibuprofen binds to both SAs in two drug-binding sites, only one of which is common. We also compare the binding of ketoprofen by equine SA to binding of it by bovine and leporine SAs. Our comparative analysis of known SA complexes with FDA-approved drugs clearly shows that multiple medications compete for the same binding sites, indicating possibilities for undesirable physiological effects caused by drug-drug displacement or competition with common metabolites. We discuss the consequences of NSAID binding to SA in a broader scientific and medical context, particularly regarding achieving desired therapeutic effects based on an individual's drug regimen.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.

Macromolecule Content 

  • Total Structure Weight: 67.16 kDa 
  • Atom Count: 4,887 
  • Modeled Residue Count: 581 
  • Deposited Residue Count: 583 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serum albumin583Equus caballusMutation(s): 1 
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9KL
(Subject of Investigation/LOI)

Query on 9KL



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
(2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid
C16 H14 O3
DKYWVDODHFEZIM-NSHDSACASA-N
KNA

Query on KNA



Download:Ideal Coordinates CCD File
E [auth A]nonanoic acid
C9 H18 O2
FBUKVWPVBMHYJY-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
UNL

Query on UNL



Download:Ideal Coordinates CCD File
H [auth A]Unknown ligand
QAOWNCQODCNURD-UHFFFAOYSA-L
UNX

Query on UNX



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
I [auth A]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.233 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.453α = 90
b = 95.453β = 90
c = 141.689γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references, Structure summary
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2020-07-15
    Changes: Database references
  • Version 1.4: 2020-07-22
    Changes: Database references
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-11-06
    Changes: Structure summary