Download MendeleyCrystal structure of spleen tyrosine kinase (Syk) in complex with SKI-O-592 (free form of SKI-O-703, cevidoplenib)
Bong, S.M., Lee, B.I.To be published.
8WYW
Crystal structure of spleen tyrosine kinase (SYK) in complex with SKI-O-592 (free form of SKI-O-703, cevidoplenib)
- PDB DOI: https://doi.org/10.2210/pdb8WYW/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2023-10-31 Released: 2024-11-06
- Funding Organization(s): National Research Foundation (NRF, Korea)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.242
- R-Value Work: 0.200
- R-Value Observed: 0.202
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tyrosine-protein kinase SYK | 293 | 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 AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| XFB (Subject of Investigation/LOI) Query on XFB | C [auth A], E [auth B] | SKI-O-592 C25 H27 N7 O3 YCZUBLQESBVOSH-IBGZPJMESA-N |  | ||
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.242
- R-Value Work: 0.200
- R-Value Observed: 0.202
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 39.719 | α = 90.034 |
| b = 39.602 | β = 90.027 |
| c = 88.355 | γ = 94.811 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-11-06 Deposition Author(s): Bong, S.M., Lee, B.I.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Research Foundation (NRF, Korea) | Korea, Republic Of | 2023R1A2C1002654 |
Revision History (Full details and data files)
- Version 1.0: 2024-11-06
Type: Initial release
