Macromolecule Content

Total Structure Weight: 34.67 kDa
Atom Count: 2576
Modelled Residue Count: 303
Deposited Residue Count: 303
Unique protein chains: 1

6HH1

Structure of c-Kit with allosteric inhibitor 3G8

PDB DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.273
R-Value Work: 0.204
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of c-Kit with allosteric inhibitor 3G8

Wrasidlo, W.J., Cheresh, D.A.

To be published.

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10721
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G4E Query on G4E Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	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		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.273
R-Value Work: 0.204
R-Value Observed: 0.208
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2018-08-24
Released Date: 2019-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.