Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 56.28 kDa 
• Atom Count: 4297 
• Modelled Residue Count: 467 
• Deposited Residue Count: 489 
• Unique protein chains: 1

5DD9

Menin in complex with MI-326

• PDB DOI: 10.2210/pdb5DD9/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-24 Released: 2015-09-09 
• Deposition Author(s): Pollock, J., Dmitry, B., Cierpicki, T., Grembecka, J.
• Funding Organization(s): American Cancer Society, National Institutes of Health/National Cancer Institute (NIH/NCI), Leukemia & Lymphoma Society, Department of Energy (DOE, United States), LS-CAT Sector 21

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.195 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes.

Pollock, J., Borkin, D., Lund, G., Purohit, T., Dyguda-Kazimierowicz, E., Grembecka, J., Cierpicki, T.

(2015) J Med Chem 58: 7465-7474

• PubMed: 26288158 
• DOI: 10.1021/acs.jmedchem.5b00975
• Primary Citation of Related Structures:  
  5DD9, 5DDA, 5DDB, 5DDC, 5DDD, 5DDE, 5DDF


• PubMed Abstract: 
  

Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein-ligand complexes. Such fluorine-backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin-MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes with menin. We found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin-MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine-backbone interactions in protein-ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin-MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine-backbone interactions may represent a particularly attractive approach to improve inhibitors of protein-protein interactions.

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Organizational Affiliation: 

Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menin	A	489	Homo sapiens	Mutation(s): 1  Gene Names: MEN1, SCG2
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens) Explore O00255  Go to UniProtKB:  O00255
PHAROS:  O00255

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
59K	B [auth A]	4-[4-(5-methyl-1,3,4-thiadiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine C15 H15 F3 N6 S2 WDNNGANTDITWSR-UHFFFAOYSA-N
PG4	E [auth A], F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	C [auth A], D [auth A], H [auth A], M [auth A], N [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
59K	Binding MOAD:  5DD9	IC50: 779 (nM) from 1 assay(s)
	BindingDB:  5DD9	IC50: 779 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.195 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.83	α = 90
b = 80.23	β = 90
c = 125.228	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-08-24 
• Released Date: 2015-09-09 
Deposition Author(s): Pollock, J., Dmitry, B., Cierpicki, T., Grembecka, J.

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Funding Organization	Location	Grant Number
American Cancer Society	United States	RSG-11-082-01-DMC
American Cancer Society	United States	RSG-13-130-01-CDD
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA181185
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA160467
Leukemia & Lymphoma Society	United States	6116-12
Leukemia & Lymphoma Society	United States	1215-14
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357
LS-CAT Sector 21	United States	085P1000817

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence