6QB4

Mcl1-scFv complex with an indole acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibody fragments structurally enable a drug-discovery campaign on the cancer target Mcl-1.

Luptak, J.Bista, M.Fisher, D.Flavell, L.Gao, N.Wickson, K.Kazmirski, S.L.Howard, T.Rawlins, P.B.Hargreaves, D.

(2019) Acta Crystallogr D Struct Biol 75: 1003-1014

  • DOI: 10.1107/S2059798319014116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Apoptosis is a crucial process by which multicellular organisms control tissue growth, removal and inflammation. Disruption of the normal apoptotic function is often observed in cancer, where cell death is avoided by the overexpression of anti-apopto ...

    Apoptosis is a crucial process by which multicellular organisms control tissue growth, removal and inflammation. Disruption of the normal apoptotic function is often observed in cancer, where cell death is avoided by the overexpression of anti-apoptotic proteins of the Bcl-2 (B-cell lymphoma 2) family, including Mcl-1 (myeloid cell leukaemia 1). This makes Mcl-1 a potential target for drug therapy, through which normal apoptosis may be restored by inhibiting the protective function of Mcl-1. Here, the discovery and biophysical properties of an anti-Mcl-1 antibody fragment are described and the utility of both the scFv and Fab are demonstrated in generating an Mcl-1 crystal system amenable to iterative structure-guided drug design.


    Organizational Affiliation

    Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Waltham, MA 02451, USA.,Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A
162Homo sapiensMutation(s): 0 
Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
scFv55
X
255N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HVN
Query on HVN

Download SDF File 
Download CCD File 
A
3-[3-[[(1~{R})-1,2,3,4-tetrahydronaphthalen-1-yl]oxy]propyl]-7-(1,3,5-trimethylpyrazol-4-yl)-1~{H}-indole-2-carboxylic acid
C28 H31 N3 O3
QINAZSGHTVBAAJ-XMMPIXPASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.947α = 90.00
b = 40.861β = 111.42
c = 77.354γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-12-20 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Hargreaves, D.

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Database references