Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.94 kDa 
• Atom Count: 2572 
• Residue Count: 314 
• Unique protein chains: 1

5VKC

Crystal structure of MCL-1 in complex with a BIM competitive inhibitor

• DOI: 10.2210/pdb5VKC/pdb

• Classification: signaling protein/inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-21 Released: 2017-05-03 
• Deposition Author(s): Judge, R.A., Souers, A.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.222 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

Structure-guided design of a series of MCL-1 inhibitors with high affinity and selectivity.

Bruncko, M., Wang, L., Sheppard, G.S., Phillips, D.C., Tahir, S.K., Xue, J., Erickson, S., Fidanze, S., Fry, E., Hasvold, L., Jenkins, G.J., Jin, S., Judge, R.A., Kovar, P.J., Madar, D., Nimmer, P., Park, C., Petros, A.M., Rosenberg, S.H., Smith, M.L., Song, X., Sun, C., Tao, Z.F., Wang, X., Xiao, Y., Zhang, H., Tse, C., Leverson, J.D., Elmore, S.W., Souers, A.J.

(2015) J Med Chem 58: 2180-2194

• PubMed: 25679114 
• DOI: 10.1021/jm501258m
• Primary Citation of Related Structures:  
  6B4U, 6B4L, 5VKC


• PubMed Abstract: 
  

Myeloid cell leukemia 1 (MCL-1) is a BCL-2 family protein that has been implicated in the progression and survival of multiple tumor types. Herein we report a series of MCL-1 inhibitors that emanated from a high throughput screening (HTS) hit and progressed via iterative cycles of structure-guided design. Advanced compounds from this series exhibited subnanomolar affinity for MCL-1 and excellent selectivity over other BCL-2 family proteins as well as multiple kinases and GPCRs. In a MCL-1 dependent human tumor cell line, administration of compound 30b rapidly induced caspase activation with associated loss in cell viability. The small molecules described herein thus comprise effective tools for studying MCL-1 biology.

---

Organizational Affiliation: 

AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Induced myeloid leukemia cell differentiation protein Mcl-1	A, B	157	Homo sapiens	Mutation(s): 0  Gene Names: MCL1, BCL2L3
Find proteins for Q07820 (Homo sapiens) Explore Q07820  Go to UniProtKB:  Q07820
NIH Common Fund Data Resources
PHAROS  Q07820 GTEx  ENSG00000143384

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9EA	A, B	7-(3-{[4-(4-acetylpiperazin-1-yl)phenoxy]methyl}-1,5-dimethyl-1H-pyrazol-4-yl)-3-{3-[(naphthalen-1-yl)oxy]propyl}-1-[(pyridin-3-yl)methyl]-1H-indole-2-carboxylic acid C46 H46 N6 O5 VKKQBUSCPZGZBT-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.222 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.92	α = 90
b = 63.92	β = 90
c = 91.4	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-04-21 
• Released Date: 2017-05-03 
Deposition Author(s): Judge, R.A., Souers, A.J.

Revision History 

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Data collection