5XY1 | pdb_00005xy1

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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

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 GTEx:  ENSG00000254087

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8H0	B [auth A]	N-(1H-indazol-6-yl)-8-piperidin-4-yloxy-6-propyl-quinazolin-2-amine C23 H26 N6 O FBHTUGHTOZWUFL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Kim, H.T.

Revision History  

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