5UJB

Structure of a Mcl-1 Inhibitor Binding to Site 3 of Human Serum Albumin

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens

  • Deposited: 2017-01-17 Released: 2017-05-03 
  • Deposition Author(s): Zhao, B.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Myeloid cell leukemia-1 (Mcl-1) inhibitor bound to drug site 3 of Human Serum Albumin.

Zhao, B.Sensintaffar, J.Bian, Z.Belmar, J.Lee, T.Olejniczak, E.T.Fesik, S.W.

(2017) Bioorg. Med. Chem. 25: 3087-3092

  • DOI: 10.1016/j.bmc.2017.03.060

  • PubMed Abstract: 
  • Amplification of the gene encoding Myeloid cell leukemia-1 (Mcl-1) is one of the most common genetic aberrations in human cancer and is associated with high tumor grade and poor survival. Recently, we reported on the discovery of high affinity Mcl-1 ...

    Amplification of the gene encoding Myeloid cell leukemia-1 (Mcl-1) is one of the most common genetic aberrations in human cancer and is associated with high tumor grade and poor survival. Recently, we reported on the discovery of high affinity Mcl-1 inhibitors that elicit mechanism-based cell activity. These inhibitors are lipophilic and contain an acidic functionality which is a common chemical profile for compounds that bind to albumin in plasma. Indeed, these Mcl-1 inhibitors exhibited reduced in vitro cell activity in the presence of serum. Here we describe the structure of a lead Mcl-1 inhibitor when bound to Human Serum Albumin (HSA). Unlike many acidic lipophilic compounds that bind to drug site 1 or 2, we found that this Mcl-1 inhibitor binds predominantly to drug site 3. Site 3 of HSA may be able to accommodate larger, more rigid compounds that do not fit into the smaller drug site 1 or 2. Structural studies of molecules that bind to this third site may provide insight into how some higher molecular weight compounds bind to albumin and could be used to aid in the design of compounds with reduced albumin binding.


    Related Citations: 
    • Discovery and biological characterization of potent myeloid cell leukemia-1 inhibitors.
      Lee, T.,Bian, Z.,Zhao, B.,Hogdal, L.J.,Sensintaffar, J.L.,Goodwin, C.M.,Belmar, J.,Shaw, S.,Tarr, J.C.,Veerasamy, N.,Matulis, S.M.,Koss, B.,Fischer, M.A.,Arnold, A.L.,Camper, D.V.,Browning, C.F.,Rossanese, O.W.,Budhraja, A.,Opferman, J.,Boise, L.H.,Savona, M.R.,Letai, A.,Olejniczak, E.T.,Fesik, S.W.
      (2016) FEBS Lett. --: --


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University, 2215 Garland Avenue, 607 Light Hall, Nashville, TN 37232-0146, USA.,Department of Biochemistry, Vanderbilt University, 2215 Garland Avenue, 607 Light Hall, Nashville, TN 37232-0146, USA. Electronic address: stephen.fesik@vanderbilt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serum albumin
A, B
609Homo 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
6AK
Query on 6AK

Download SDF File 
Download CCD File 
A, B
4-{8-chloro-11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1,4]diazepino[1,2-a]indol-2(3H)-yl}-1-methyl-1H-indole-6-carboxylic acid
C39 H39 Cl2 N5 O4
BDINUPBROUJUMH-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.844α = 90.00
b = 182.338β = 105.15
c = 58.925γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-17 
  • Released Date: 2017-05-03 
  • Deposition Author(s): Zhao, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesBOA 29XS129

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence