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 

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Ligand Structure Quality Assessment 


This is version 1.1 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)
Explore P02768 
Go to UniProtKB:  P02768
PHAROS:  P02768
GTEx:  ENSG00000163631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
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  • 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
Binding Affinity Annotations 
IDSourceBinding Affinity
C7K Binding MOAD:  6EZQ Kd: 1.40e+4 (nM) from 1 assay(s)
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

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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