8BSG | pdb_00008bsg

COMPLEX OF LEPORINE SERUM ALBUMIN WITH DICLOFENAC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.201 (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 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4F5V 6OCK 6OCL 4PO0

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: 68.14 kDa 
  • Atom Count: 5,163 
  • Modeled Residue Count: 584 
  • Deposited Residue Count: 584 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Albumin584Oryctolagus cuniculusMutation(s): 0 
Gene Names: ALB
UniProt
Find proteins for P49065 (Oryctolagus cuniculus)
Explore P49065 
Go to UniProtKB:  P49065
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49065
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POG

Query on POG



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
(20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL
C21 H44 O8
OWRNLGZKEZSHGO-QAWAPDBNSA-N
DIF
(Subject of Investigation/LOI)

Query on DIF



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

Query on PGO



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A]
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
N [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.78α = 90
b = 80.13β = 90
c = 104.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

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/T5/02271

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Structure summary