5XY1

Crystal structure of Lyn kinase domain in complex with N-(1H-indazol-6-yl)-8-(piperidin-4-yloxy)-6-propylquinazolin-2-amine

PDB DOI: https://doi.org/10.2210/pdb5XY1/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2017-07-05 Released: 2017-08-02
Deposition Author(s): Kim, H.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.260
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Lyn kinase domain in complex with N-(1H-indazol-6-yl)-8-(piperidin-4-yloxy)-6-propylquinazolin-2-amine

Kim, H.T.

To be published.

Macromolecule Content

Total Structure Weight: 32.2 kDa
Atom Count: 2,070
Modelled Residue Count: 253
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Lyn	A	279	Homo sapiens	Mutation(s): 0 Gene Names: LYN, JTK8 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07948 (Homo sapiens) Explore P07948 Go to UniProtKB: P07948
PHAROS: P07948
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07948
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8H0 Query on 8H0 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-(1H-indazol-6-yl)-8-piperidin-4-yloxy-6-propyl-quinazolin-2-amine C₂₃ H₂₆ N₆ O FBHTUGHTOZWUFL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.260
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.864	α = 90
b = 128.864	β = 90
c = 55.123	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are 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.