3B9L

Human serum albumin complexed with myristate and AZT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new drug binding subsite on human serum albumin and drug-drug interaction studied by X-ray crystallography

Zhu, L.Yang, F.Chen, L.Meehan, E.J.Huang, M.

(2008) J.Struct.Biol. 162: 40-49

  • DOI: 10.1016/j.jsb.2007.12.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 3'-Azido-3'-deoxythymidine (AZT) is the first clinically effective drug for the treatment of human immunodeficiency virus infection. The drug interaction with human serum albumin (HSA) has been an important component in understanding its mechanism of ...

    3'-Azido-3'-deoxythymidine (AZT) is the first clinically effective drug for the treatment of human immunodeficiency virus infection. The drug interaction with human serum albumin (HSA) has been an important component in understanding its mechanism of action, especially in drug distribution and in drug-drug interaction on HSA in the case of multi-drug therapy. We present here crystal structures of a ternary HSA-Myr-AZT complex and a quaternary HSA-Myr-AZT-SAL complex (Myr, myristate; SAL, salicylic acid). From this study, a new drug binding subsite on HSA Sudlow site 1 was identified. The presence of fatty acid is needed for the creation of this subsite due to fatty acid induced conformational changes of HSA. Thus, the Sudlow site 1 of HSA can be divided into three non-overlapped subsites: a SAL subsite, an indomethacin subsite and an AZT subsite. Binding of a drug to HSA often influences simultaneous binding of other drugs. From the HSA-Myr-AZT-SAL complex structure, we observed the coexistence of two drugs (AZT and SAL) in Sudlow site 1 and the competition between these two drugs in subdomain IB. These results provide new structural information on HSA-drug interaction and drug-drug interaction on HSA.


    Related Citations: 
    • Structural basis of the drug-binding specificity of human serum albumin
      Ghuman, J.,Zunszain, P.A.,Petitpas, I.,Bhattacharya, A.A.,Otagiri, M.,Curry, S.
      (2005) J.Mol.Biol. 353: 38
    • Atomic structure and chemistry of human serum albumin
      He, X.M.,Carter, D.C.
      (1992) Nature 358: 209
    • Effect of human serum albumin on drug metabolism: structural evidence of esterase activity of human serum albumin
      Yang, F.,Bian, C.,Zhu, L.,Zhao, G.,Huang, Z.,Huang, M.
      (2007) J.Struct.Biol. 157: 348


    Organizational Affiliation

    State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, The Chinese Academy of Sciences, 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002, China. zhulili@fjirsm.ac.cn




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serum albumin
A
585Homo sapiensMutation(s): 0 
Gene Names: ALB
Find proteins for P02768 (Homo sapiens)
Go to Gene View: ALB
Go to UniProtKB:  P02768
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
A
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
AZZ
Query on AZZ

Download SDF File 
Download CCD File 
A
3'-azido-3'-deoxythymidine
Azidothymidine; Zidovudine
C10 H13 N5 O4
HBOMLICNUCNMMY-XLPZGREQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZZKd: 0.4 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 183.900α = 90.00
b = 38.696β = 104.35
c = 95.867γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSrefinement
CNSphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-07-18
    Type: Non-polymer description