6ZCP

SYK Kinase domain in complex with azabenzimidazole inhibitor 2b

• PDB DOI: https://doi.org/10.2210/pdb6ZCP/pdb

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


• Deposited: 2020-06-11 Released: 2021-06-23 
• Deposition Author(s): Read, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

SYK Kinase domain in complex with azabenzimidazole inhibitor 4

Read, J.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.29 kDa 
• Atom Count: 2,198 
• Modelled Residue Count: 267 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QFK (Subject of Investigation/LOI)	B [auth A]	7-[[4-[4-[(dimethylamino)methyl]pyrazol-1-yl]pyrimidin-2-yl]amino]-~{N},3-dimethyl-imidazo[1,5-a]pyridine-1-carboxamide C20 H23 N9 O PLXRPQJOIKHDDA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.93	α = 90
b = 85.62	β = 90
c = 89.83	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Read, J.A.

Revision History  

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