6ITV | pdb_00006itv

Crystal structure of activated c-KIT in complex with compound

PDB DOI: https://doi.org/10.2210/pdb6ITV/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2018-11-26 Released: 2019-11-27
Deposition Author(s): Wu, T.S., Wu, S.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.231 (Depositor), 0.227 (DCC)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.183 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of activated c-KIT in complex with compound

Wu, T.S., Wu, S.Y.

To be published.

Macromolecule Content

Total Structure Weight: 38.27 kDa
Atom Count: 2,646
Modeled Residue Count: 298
Deposited Residue Count: 331
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor Kit	A	331	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AWO Query on AWO 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]	N-(5-ethyl-1,2-oxazol-3-yl)-N'-[4-(2-{[6-(4-ethylpyrazin-1(4H)-yl)pyrimidin-4-yl]amino}-1,3-thiazol-5-yl)phenyl]urea C₂₅ H₂₅ N₉ O₂ S UPVPVNFMFOJQIG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.231 (Depositor), 0.227 (DCC)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.853	α = 90
b = 59.853	β = 90
c = 197.984	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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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.