8GWW | pdb_00008gww

Small-molecule Allosteric Regulation Mechanism of SHP2

PDB DOI: https://doi.org/10.2210/pdb8GWW/pdb

Classification: ONCOPROTEIN/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-17 Released: 2023-09-20
Deposition Author(s): Luo, Y., Zhu, J., Yu, K., Liu, B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.288 (Depositor), 0.284 (DCC)
R-Value Work:
0.240 (Depositor), 0.237 (DCC)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Small-molecule Allosteric Regulation Mechanism of SHP2

Luo, Y., Zhu, J., Yu, K., Liu, B.

To be published.

Macromolecule Content

Total Structure Weight: 121.34 kDa
Atom Count: 7,386
Modeled Residue Count: 955
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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: 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06124
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KID (Subject of Investigation/LOI) Query on KID Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	2-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-5-[2,3-bis(chloranyl)phenyl]-3-methyl-pyrrolo[2,1-f][1,2,4]triazin-4-one C₂₀ H₂₃ Cl₂ N₅ O CURVWOSSQXPKOR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.288 (Depositor), 0.284 (DCC)
R-Value Work: 0.240 (Depositor), 0.237 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.499	α = 90
b = 91.17	β = 90
c = 213.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-09-20
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.