5KU9

Crystal structure of MCL1 with compound 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 

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.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:  

  • 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
A, B
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
6XJ
Query on 6XJ
Download SDF File 
Download CCD File 
A, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6XJIC50: 1490 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.381α = 90.00
b = 60.647β = 121.15
c = 69.087γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
BUSTERrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History 

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