6QB4

Mcl1-scFv complex with an indole acid inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6QB4/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Cricetulus griseus
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.231 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

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

• PubMed: 31692474 
• DOI: https://doi.org/10.1107/S2059798319014116
• Primary Citation of Related Structures:  
  6QB3, 6QB4, 6QB6, 6QB9, 6QBC, 6QF9, 6QFC


• 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-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, Cambridge CB4 0WG, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.11 kDa 
• Atom Count: 3,062 
• Modelled Residue Count: 373 
• Deposited Residue Count: 417 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Induced myeloid leukemia cell differentiation protein Mcl-1	A	162	Homo sapiens	Mutation(s): 0  Gene Names: MCL1, BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens) Explore Q07820  Go to UniProtKB:  Q07820
PHAROS:  Q07820 GTEx:  ENSG00000143384

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv55	B [auth X]	255	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HVN	C [auth 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.231 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.947	α = 90
b = 40.861	β = 111.42
c = 77.354	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary