5MEV

MCL1 FAB COMPLEX IN COMPLEX WITH COMPOUND 21

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structure Based Design of Non-Natural Peptidic Macrocyclic Mcl-1 Inhibitors

Johannes, J.W., Bates, S., Beigie, C., Belmonte, M., Breen, J., Cao, S., Centrella, P.A., Clark, M.A., Cuozzo, J.W., Dumelin, C.E., Ferguson, A.D., Habeshian, S., Hargreaves, D., Joubran, C., Kazmirski, S., Keefe, A., Lamb, M.L., Lan, H., Li, Y., Ma, H., Mlynarski, S., Packer, M.J., Rawlins, P., Robbins, D.W., Shen, H., Sigel, E.A., Soutter, H.H., Su, N., Trost, D.M., Wang, H., Wickson, K.F., Wu, C., Zhang, Y., Zhao, Q., Zheng, X., Hird, A.

(2017) Acs Med.Chem.Lett. 8: 239-244

  • DOI: 10.1021/acsmedchemlett.6b00464
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Mcl-1 is a pro-apoptotic BH3 protein family member similar to Bcl-2 and Bcl-xL. Overexpression of Mcl-1 is often seen in various tumors and allows cancer cells to evade apoptosis. Here we report the discovery and optimization of a series of non-natur ...

    Mcl-1 is a pro-apoptotic BH3 protein family member similar to Bcl-2 and Bcl-xL. Overexpression of Mcl-1 is often seen in various tumors and allows cancer cells to evade apoptosis. Here we report the discovery and optimization of a series of non-natural peptide Mcl-1 inhibitors. Screening of DNA-encoded libraries resulted in hit compound 1 , a 1.5 μM Mcl-1 inhibitor. A subsequent crystal structure demonstrated that compound 1 bound to Mcl-1 in a β-turn conformation, such that the two ends of the peptide were close together. This proximity allowed for the linking of the two ends of the peptide to form a macrocycle. Macrocyclization resulted in an approximately 10-fold improvement in binding potency. Further exploration of a key hydrophobic interaction with Mcl-1 protein and also with the moiety that engages Arg256 led to additional potency improvements. The use of protein-ligand crystal structures and binding kinetics contributed to the design and understanding of the potency gains. Optimized compound 26 is a <3 nM Mcl-1 inhibitor, while inhibiting Bcl-2 at only 5 μM and Bcl-xL at >99 μM, and induces cleaved caspase-3 in MV4-11 cells with an IC 50 of 3 μM after 6 h.

    Organizational Affiliation: 

    X-Chem Pharmaceuticals , 100 Beaver Street, Waltham, Massachusetts 02453, United States.,AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.,Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China.,AstraZeneca R&D Cambridge Science Park , Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom.,AstraZeneca R&D Alderley Park , Macclesfield, Cheshire SK10 4TG, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1
A
162Homo sapiens, Mus musculus
This entity is chimeric		Mutation(s): 0 
Gene Names: MCL1 (BCL2L3), Mcl1
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Find proteins for P97287 (Mus musculus)
Go to UniProtKB:  P97287
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab Heavy Chain
H
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab Light Chain
L
226N/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
7LW
Query on 7LW
Download SDF File 
Download CCD File 
A
(5~{R},13~{S},17~{S})-5-[(3,4-dichlorophenyl)methyl]-8-methyl-13-[(4-methylsulfonylphenyl)methyl]-1,4,8,12,16-pentazatricyclo[15.8.1.0^{20,25}]hexacosa-20,22,24-triene-3,7,15,26-tetrone
C37 H43 Cl2 N5 O6 S
FBRYDBXOEZYXPV-NGKQEFFVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 166.514α = 90.00
b = 39.705β = 125.74
c = 103.515γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-11-16 
  • Released Date: 2017-01-18 
  • Deposition Author(s): Hargreaves, D.

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-03-08
    Type: Database references