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 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


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:  
    5KU9, 5MES, 5MEV

  • 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-natural peptide Mcl-1 inhibitors ...

    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: 

    AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1A162Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: Mcl1, BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for P97287 (Mus musculus)
Explore P97287 
Go to UniProtKB:  P97287
IMPC:  MGI:101769
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
GTEx:  ENSG00000143384 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP97287Q07820
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Heavy ChainB [auth H]230Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Light ChainC [auth L]226Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7LW
Query on 7LW
Download Ideal Coordinates CCD File 
D [auth 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 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.514α = 90
b = 39.705β = 125.74
c = 103.515γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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