4WGI | pdb_00004wgi

A Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia 1 (MCL1)

• PDB DOI: https://doi.org/10.2210/pdb4WGI/pdb

• Classification: apoptosis/inhibitor
• Organism(s): Escherichia coli O157:H7, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-09-18 Released: 2014-11-19 
• Deposition Author(s): Clifton, M.C., Fairman, J.W., Fang, C., D'Souza, B., Fulroth, B., Leed, A., McCarren, P., Wang, L., Wang, Y., Kaushik, V., Palmer, M., Wei, G., Golub, T.R., Hubbard, B.K., Serrano-Wu, M.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia 1 (MCL1).

Fang, C., D'Souza, B., Thompson, C.F., Clifton, M.C., Fairman, J.W., Fulroth, B., Leed, A., McCarren, P., Wang, L., Wang, Y., Feau, C., Kaushik, V.K., Palmer, M., Wei, G., Golub, T.R., Hubbard, B.K., Serrano-Wu, M.H.

(2014) ACS Med Chem Lett 5: 1308-1312

• PubMed: 25516789 
• DOI: https://doi.org/10.1021/ml500388q
• Primary Citation Related Structures: 
  4WGI


• PubMed Abstract: 
  

  A direct binding screen of 100 000 sp(3)-rich molecules identified a single diastereomer of a macrolactam core that binds specifically to myeloid cell leukemia 1 (MCL1). A comprehensive toolbox of biophysical methods was applied to validate the original hit and subsequent analogues and also established a binding mode competitive with NOXA BH3 peptide. X-ray crystallography of ligand bound to MCL1 reveals a remarkable ligand/protein shape complementarity that diverges from previously disclosed MCL1 inhibitor costructures.

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Organizational Affiliation: 
• Broad Institute , 415 Main Street, Cambridge, Massachusetts 02142, United States.
Beryllium , 3 Preston Court, Bedford, Massachusetts 01730, United States.
Broad Institute , 415 Main Street, Cambridge, Massachusetts 02142, United States ; Dana-Farber Cancer Institute and Howard Hughes Medical Institute , 450 Brookline Avenue, Boston, Massachusetts 02215, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.8 kDa 
• Atom Count: 4,507 
• Modeled Residue Count: 513 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1	A	518	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: malE, Z5632, ECs5017, MCL1, BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0  Go to UniProtKB:  P0AEY0
Find proteins for Q07820 (Homo sapiens) Explore Q07820  Go to UniProtKB:  Q07820
PHAROS:  Q07820 GTEx:  ENSG00000143384
UniProt Groups	P0AEY0Q07820

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3M6	C [auth A]	(2S)-2-[(2S,3R)-10-{[(4-fluorophenyl)sulfonyl]amino}-3-methyl-2-[(methyl{[4-(trifluoromethyl)phenyl]carbamoyl}amino)methyl]-6-oxo-3,4-dihydro-2H-1,5-benzoxazocin-5(6H)-yl]propanoic acid C30 H30 F4 N4 O7 S XAEPMFMCFFIZDH-FUMQJTLXSA-N
FMT	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3M6	BindingDB:  4WGI	Kd: min: 1900, max: 6000 (nM) from 2 assay(s)
		IC50: 4500 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.3	α = 90
b = 135.87	β = 90
c = 37.69	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Clifton, M.C., Fairman, J.W., Fang, C., D'Souza, B., Fulroth, B., Leed, A., McCarren, P., Wang, L., Wang, Y., Kaushik, V., Palmer, M., Wei, G., Golub, T.R., Hubbard, B.K., Serrano-Wu, M.H.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary