4GFG | pdb_00004gfg

Crystal structure of spleen tyrosine kinase complexed with r9021

PDB DOI: https://doi.org/10.2210/pdb4GFG/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2012-08-03 Released: 2013-08-14
Deposition Author(s): Lukacs, C., Slade, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.246 (Depositor), 0.244 (DCC)
R-Value Work:
0.219 (Depositor), 0.214 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A specific SYK inhibitor blocks B Cell Receptor, Fc Receptor, and Toll-like Receptor 9 pathways for the treatment of inflammatory diseases.

Hsu, J., Kim, Y., Hu, D.-Q., Xu, D., Zhang, J., Pashine, A., Menke, J., Whittard, T., Romero, N., Truitt, T., Lukacs, C., Zhou, M., Lucas, M., Slade, M., DeMartino, J., Tan, S.-L., Liao, C.

To be published.

Macromolecule Content

Total Structure Weight: 34.24 kDa
Atom Count: 2,379
Modeled Residue Count: 277
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	291	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0XF Query on 0XF 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]	6-{[(1R,2S)-2-aminocyclohexyl]amino}-4-[(5,6-dimethylpyridin-2-yl)amino]pyridazine-3-carboxamide C₁₈ H₂₅ N₇ O XJZVCDVZCRLIKN-QWHCGFSZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
0XF	BindingDB: 4GFG	IC50: min: 5, max: 32 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.246 (Depositor), 0.244 (DCC)
R-Value Work: 0.219 (Depositor), 0.214 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.061	α = 90
b = 85.647	β = 90
c = 90.93	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
CNX	refinement
XDS	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-14
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, 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.