8WFY | pdb_00008wfy

The Crystal Structure of SHP2 from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8WFY/pdb

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


• Deposited: 2023-09-20 Released: 2023-11-22 
• Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.317 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of SHP2 from Biortus.

Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 121.07 kDa 
• Atom Count: 8,400 
• Modeled Residue Count: 980 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 11	A, B	525	Homo sapiens	Mutation(s): 0  Gene Names: PTPN11 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens) Explore Q06124  Go to UniProtKB:  Q06124
PHAROS:  Q06124 GTEx:  ENSG00000179295

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5OD (Subject of Investigation/LOI)	C [auth A], D [auth B]	6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine C16 H19 Cl2 N5 YGUFCDOEKKVKJK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5OD	BindingDB:  8WFY	Ki: 67 (nM) from 1 assay(s)
		Kd: min: 73, max: 1500 (nM) from 2 assay(s)
		IC50: min: 0.14, max: 677 (nM) from 14 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.317 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.617	α = 90
b = 213.636	β = 96.846
c = 55.707	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release