6ZCX

SYK Kinase domain in complex with azabenzimidazole inhibitor 18

PDB DOI: https://doi.org/10.2210/pdb6ZCX/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-12 Released: 2021-06-23
Deposition Author(s): Read, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.229
R-Value Work: 0.189
R-Value Observed: 0.191

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SYK Kinase domain in complex with azabenzimidazole inhibitor 18

Read, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 35.34 kDa
Atom Count: 2,427
Modelled Residue Count: 266
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	299	Homo sapiens	Mutation(s): 0 Gene Names: SYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens) Explore P43405 Go to UniProtKB: P43405
PHAROS: P43405 GTEx: ENSG00000165025
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QFQ (Subject of Investigation/LOI) Query on QFQ 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},1-dimethyl-5-[[4-[3-methyl-4-[[(3~{R})-piperidin-3-yl]amino]pyrazol-1-yl]pyrimidin-2-yl]amino]indazole-3-carboxamide C₂₃ H₂₈ N₁₀ O CGMCYALTKDQISD-MRXNPFEDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.229
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.548	α = 90
b = 85.461	β = 90
c = 90.019	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-23
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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.