7SI4 | pdb_00007si4

CRYSTAL STRUCTURE OF EED WITH MRTX-2219

• PDB DOI: https://doi.org/10.2210/pdb7SI4/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-12 Released: 2022-11-09 
• Deposition Author(s): Gunn, R.J., Burns, A.C., Lawson, J.D., Marx, M.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF EED WITH MRTX-2219

Burns, A.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.71 kDa 
• Atom Count: 3,256 
• Modeled Residue Count: 360 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein EED	A	402	Homo sapiens	Mutation(s): 0  Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens) Explore O75530  Go to UniProtKB:  O75530
PHAROS:  O75530 GTEx:  ENSG00000074266

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JL (Subject of Investigation/LOI)	B [auth A]	(4S)-8-{4-[(dimethylamino)methyl]-2-methylphenyl}-5-{[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]amino}imidazo[1,2-c]pyrimidine-2-carbonitrile C26 H25 F N6 O FLCIOLFIDGTRCI-UHFFFAOYSA-N
FMT	C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9JL	BindingDB:  7SI4	IC50: min: 100, max: 300 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.658	α = 90
b = 85.279	β = 90
c = 91.236	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Gunn, R.J., Burns, A.C., Lawson, J.D., Marx, M.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description