6HH1 | pdb_00006hh1

Structure of c-Kit with allosteric inhibitor 3G8

• PDB DOI: https://doi.org/10.2210/pdb6HH1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-08-24 Released: 2019-09-18 
• Deposition Author(s): Wrasidlo, W.J., Cheresh, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Structure of c-Kit with allosteric inhibitor 3G8

Wrasidlo, W.J., Cheresh, D.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.67 kDa 
• Atom Count: 2,576 
• Modeled Residue Count: 303 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit	A	303	Homo sapiens	Mutation(s): 0  Gene Names: KIT, SCFR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens) Explore P10721  Go to UniProtKB:  P10721
PHAROS:  P10721 GTEx:  ENSG00000157404

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4E	C [auth A]	~{N}-(2,3-dimethylphenyl)-5-(4-pyridin-4-yloxyphenyl)-4~{H}-1,2,4-triazol-3-amine C21 H19 N5 O FRUZWHLTFSTCFH-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.614	α = 90
b = 65.614	β = 90
c = 159.004	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Wrasidlo, W.J., Cheresh, D.A.

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references