6HN0 | pdb_00006hn0

Complex of Ovine Serum Albumin with diclofenac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.167 (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 2.3 of the entry. See complete history

Literature

Structural Investigation of Diclofenac Binding to Ovine, Caprine, and Leporine Serum Albumins.

Talaj, J.A.Zielinski, K.Bujacz, A.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24021534
  • Primary Citation Related Structures: 
    6HN0, 6HN1, 8BSG

  • PubMed Abstract: 

    Free drug concentration in the blood sera is crucial for its appropriate activity. Serum albumin, the universal blood carrier protein, is responsible for transporting drugs and releasing them into the bloodstream. Therefore, a drug's binding to SA is especially important for its bioavailability and it is a key problem in the drug design process. In this paper, we present crystal structures of three animal serum albumin complexes: ovine, caprine, and leporine, with diclofenac, a popular non-steroidal anti-inflammatory drug that is used in therapy of chronic and acute pain. Details of diclofenac binding mode by the presented serum albumins are compared with analogous complexes of human and equine serum albumins. The analysis of the occupied binding pockets in crystal structures of the investigated serum albumins from different mammals shows that they have two common and a number of unique diclofenac binding sites. The most intriguing is the fact that the albumins from the described species are able to bind different numbers of molecules of this popular anti-inflammatory drug, but none of the binding sites overlap with ones in the human serum albumin.


  • Organizational Affiliation
    • Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215 Lodz, Poland.

Macromolecule Content 

  • Total Structure Weight: 69.27 kDa 
  • Atom Count: 5,467 
  • Modeled Residue Count: 583 
  • Deposited Residue Count: 583 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serum albumin583Ovis ariesMutation(s): 0 
UniProt
Find proteins for P14639 (Ovis aries)
Explore P14639 
Go to UniProtKB:  P14639
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14639
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DIF
(Subject of Investigation/LOI)

Query on DIF



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
C14 H11 Cl2 N O2
DCOPUUMXTXDBNB-UHFFFAOYSA-N
LMR

Query on LMR



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
MLI

Query on MLI



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

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT

Query on FMT



Download:Ideal Coordinates CCD File
M [auth A]
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.68α = 90
b = 121.68β = 90
c = 121.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2013/11/B/ST5/02271

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 2.0: 2022-12-07
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-02-08
    Changes: Database references
  • Version 2.2: 2024-02-07
    Changes: Data collection
  • Version 2.3: 2024-10-23
    Changes: Structure summary