3O5X

Crystal structure of the oncogenic tyrosine phosphatase SHP2 complexed with a salicylic acid-based small molecule inhibitor

Structural Biology Knowledgebase: 3O5X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3O5X

Classification: HYDROLASE

Total Structure Weight: 32835.55

Macromolecule Entities
Molecule Chains Length Organism Details
Tyrosine-protein phosphatase non-receptor type 11 A 276 Homo sapiens EC#: 3.1.3.48 IUBMB
Fragment: UNP RESIDUES 262-532, CATALYTIC DOMAIN
Mutation: ΔQ408, ΔA409, ΔL410, ΔL411
Gene Name(s): PTPN11 Gene View PTP2C SHPTP2

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
JZG
Query on JZG

A 3-{1-[3-(biphenyl-4-ylamino)-3-oxopropyl]- 1H-1,2,3-triazol-4-yl}-6-hydroxy-1-methyl- 2-phenyl-1H-indole-5-carboxylic acid
C33 H27 N5 O4
RATFAFAWIWHLMR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
JZG IC50: 5500 nM (97) BindingDB
Ki: 5200 nM (97) BindingDB

IC50: 5500 nM  BindingMOAD
Ki: 5200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.196
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 39.54 α = 90.00
b = 75.83 β = 98.53
c = 48.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-07-28
  • Released Date: 2010-08-11
  • Deposition author(s): Zhang, Z.-Y., Zhang, X., He, Y., Liu, S., Yu, Z., Jiang, Z., Yang, Z., Dong, Y., Nabinger, S.C., Wu, L., Gunawan, A.M., Wang, L., Chan, R.J.
  • Previous versions: 3JRL

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4