MCL1 in complex with an indole acid ligand

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 

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Discovery of Mcl-1-specific inhibitor AZD5991 and preclinical activity in multiple myeloma and acute myeloid leukemia.

Tron, A.E.Belmonte, M.A.Adam, A.Aquila, B.M.Boise, L.H.Chiarparin, E.Cidado, J.Embrey, K.J.Gangl, E.Gibbons, F.D.Gregory, G.P.Hargreaves, D.Hendricks, J.A.Johannes, J.W.Johnstone, R.W.Kazmirski, S.L.Kettle, J.G.Lamb, M.L.Matulis, S.M.Nooka, A.K.Packer, M.J.Peng, B.Rawlins, P.B.Robbins, D.W.Schuller, A.G.Su, N.Yang, W.Ye, Q.Zheng, X.Secrist, J.P.Clark, E.A.Wilson, D.M.Fawell, S.E.Hird, A.W.

(2018) Nat Commun 9: 5341-5341

  • DOI: https://doi.org/10.1038/s41467-018-07551-w
  • Primary Citation of Related Structures:  
    6FS0, 6FS1, 6FS2

  • PubMed Abstract: 

    Mcl-1 is a member of the Bcl-2 family of proteins that promotes cell survival by preventing induction of apoptosis in many cancers. High expression of Mcl-1 causes tumorigenesis and resistance to anticancer therapies highlighting the potential of Mcl-1 inhibitors as anticancer drugs. Here, we describe AZD5991, a rationally designed macrocyclic molecule with high selectivity and affinity for Mcl-1 currently in clinical development. Our studies demonstrate that AZD5991 binds directly to Mcl-1 and induces rapid apoptosis in cancer cells, most notably myeloma and acute myeloid leukemia, by activating the Bak-dependent mitochondrial apoptotic pathway. AZD5991 shows potent antitumor activity in vivo with complete tumor regression in several models of multiple myeloma and acute myeloid leukemia after a single tolerated dose as monotherapy or in combination with bortezomib or venetoclax. Based on these promising data, a Phase I clinical trial has been launched for evaluation of AZD5991 in patients with hematological malignancies (NCT03218683).

  • Organizational Affiliation

    Oncology, IMED Biotech Unit, AstraZeneca, Waltham, MA, 02451, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B
150Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
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 GroupQ07820
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on E4Q

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
7-[3-[(1,5-dimethylpyrazol-3-yl)methylsulfanylmethyl]-1,5-dimethyl-pyrazol-4-yl]-3-(3-naphthalen-1-yloxypropyl)-1~{H}-indole-2-carboxylic acid
C34 H35 N5 O3 S
Query on EDO

Download Ideal Coordinates CCD File 
D [auth B],
E [auth B]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
E4Q Binding MOAD:  6FS1 Kd: 98 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.68α = 90
b = 64.519β = 98.82
c = 59.975γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release