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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.273 (Depositor), 0.274 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure of c-Kit with allosteric inhibitor 3G8

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10721
Sequence Annotations 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] mmCIF 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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.273 (Depositor), 0.274 (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

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Entry History

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.