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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.260 (Depositor), 0.256 (DCC)
R-Value Work:
0.214 (Depositor), 0.215 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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
Modeled Residue Count: 253
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.256 (DCC)
R-Value Work: 0.214 (Depositor), 0.215 (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

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Ligand Structure Quality Assessment

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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

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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.