8XQ0 | pdb_00008xq0

Crystal structure of spleen tyrosine kinase(SYK)in complex with SKI-G-1653

• PDB DOI: https://doi.org/10.2210/pdb8XQ0/pdb

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


• Deposited: 2024-01-04 Released: 2025-01-15 
• Deposition Author(s): Bong, S.M., Lee, B.I.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spleen tyrosine kinase(SYK) in complex with SKI-G-1673

Lee, B.I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 137.61 kDa 
• Atom Count: 8,818 
• Modeled Residue Count: 1,038 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A, B, C, D	290	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
A1LV4 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	cyclopropyl-[5-[[4-[4-[[(3~{S},4~{S})-3-methoxy-4-oxidanyl-pyrrolidin-1-yl]methyl]-3-methyl-pyrazol-1-yl]pyrimidin-2-yl]amino]-1-methyl-indol-3-yl]methanone C27 H31 N7 O3 CBNDBWHBUUWRCT-ZEQRLZLVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.759	α = 90.005
b = 85.262	β = 85.195
c = 79.573	γ = 90.031

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Bong, S.M., Lee, B.I.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release