5KU9

Crystal structure of MCL1 with compound 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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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.A., 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.D., Lamb, M.L., Lan, H., Li, Y., Ma, H., Mlynarski, S., Packer, M.J., Rawlins, P.B., Robbins, D.W., Shen, H., Sigel, E.A., Soutter, H.H., Su, N., Troast, D.M., Wang, H., Wickson, K.F., Wu, C., Zhang, Y., Zhao, Q., Zheng, X., Hird, A.W.

(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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1A, B162Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: Mcl1, BCL2L3
EC: 3.6.1.11
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP97287Q07820
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XJ
Query on 6XJ
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]		(3~{S})-3-azanyl-4-(4-bromophenyl)-~{N}-[(3~{S})-1-[2-[[(2~{R})-1-(3,4-dichlorophenyl)-4-(methylamino)-4-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]-2-oxidanylidene-4,5-dihydro-3~{H}-1-benzazepin-3-yl]butanamide
C33 H36 Br Cl2 N5 O4
CCMSKSUYUVJSCD-OARDWFSCSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6XJ Binding MOAD:  5KU9 IC50: 1490 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.381α = 90
b = 60.647β = 121.15
c = 69.087γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2016-07-13 
  • Released Date: 2017-01-11 
    • Deposition Author(s): Ferguson, A.D.

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Structure summary