4PVG

Crystal structure of protein tyrosine phosphatase Shp2 catalytic domain complex with small molecular compound L88N79

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of protein tyrosine Shp2 catalytic domain complex with compound L88N79

Zhang, Z.-Y., Zeng, L., Liu, D., Yu, Z.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11298Homo sapiensMutation(s): 0 
Gene Names: PTPN11, PTP2C, SHPTP2
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06124
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2WT
Query on 2WT
Download Ideal Coordinates CCD File 
B [auth A]2-[3-({4-[(1,3-benzodioxol-5-ylmethyl)amino]-4-oxobutanoyl}amino)phenyl]-6-hydroxy-3-iodo-1-methyl-1H-indole-5-carboxylic acid
C28 H24 I N3 O7
RYALHYUYZACQOT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2WT BindingDB:  4PVG IC50: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.031α = 94.58
b = 40.921β = 109.19
c = 48.934γ = 109.95
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description