6EZQ

human Serum Albumin complexed with NBD-C12 fatty acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification and Characterization of a Single High-Affinity Fatty Acid Binding Site in Human Serum Albumin.

Wenskowsky, L.Schreuder, H.Derdau, V.Matter, H.Volkmar, J.Nazare, M.Opatz, T.Petry, S.

(2018) Angew Chem Int Ed Engl 57: 1044-1048

  • DOI: https://doi.org/10.1002/anie.201710437
  • Primary Citation of Related Structures:  
    6EZQ

  • PubMed Abstract: 

    A single high-affinity fatty acid binding site in the important human transport protein serum albumin (HSA) is identified and characterized using an NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl)-C 12 fatty acid. This ligand exhibits a 1:1 binding stoichiometry in its HSA complex with high site-specificity. The complex dissociation constant is determined by titration experiments as well as radioactive equilibrium dialysis. Competition experiments with the known HSA-binding drugs warfarin and ibuprofen confirm the new binding site to be different from Sudlow-sites I and II. These binding studies are extended to other albumin binders and fatty acid derivatives. Furthermore an X-ray crystal structure allows locating the binding site in HSA subdomain IIA. The knowledge about this novel HSA site will be important for drug depot development and for understanding drug-protein interaction, which are important prerequisites for modulation of drug pharmacokinetics.


  • Organizational Affiliation

    Institute of Organic Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128, Mainz, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serum albumin585Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Go to UniProtKB:  P02768
PHAROS:  P02768
GTEx:  ENSG00000163631 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C7K
Query on C7K

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
12-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]dodecanoic acid
C18 H26 N4 O5
YPOHVKMXKUSZRL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.48α = 90
b = 52.72β = 110.1
c = 123.3γ = 90
Software Package:
Software NamePurpose
autoPROCdata collection
XDSdata reduction
XDSdata reduction
autoPROCdata scaling
STARANISOdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Refinement description, Structure summary