6BXH | pdb_00006bxh

Menin in complex with MI-853

• PDB DOI: https://doi.org/10.2210/pdb6BXH/pdb

• Classification: Protein Binding, Transcription
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-11-28 
• Deposition Author(s): Borkin, D., Klossowski, S., Pollock, J., Linhares, B., Cierpicki, T., Grembecka, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.255 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Menin in complex with MI-853

Borkin, D., Klossowski, S., Pollock, J., Linhares, B., Cierpicki, T., Grembecka, J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 57.46 kDa 
• Atom Count: 3,869 
• Modeled Residue Count: 468 
• Deposited Residue Count: 509 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menin	A	509	Homo sapiens	Mutation(s): 0  Gene Names: MEN1, SCG2
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens) Explore O00255  Go to UniProtKB:  O00255
PHAROS:  O00255 GTEx:  ENSG00000133895

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EE7 (Subject of Investigation/LOI)	D [auth A]	1-{2-[4-(fluoroacetyl)piperazin-1-yl]ethyl}-4-methyl-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile C32 H36 F4 N8 O S LEXHBKLOMBAPDX-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EE7	BindingDB:  6BXH	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.255 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.034	α = 90
b = 78.118	β = 90
c = 121.326	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Borkin, D., Klossowski, S., Pollock, J., Linhares, B., Cierpicki, T., Grembecka, J.

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description