Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 43.81 kDa 
• Atom Count: 2754 
• Modelled Residue Count: 337 
• Deposited Residue Count: 380 
• Unique protein chains: 1

5XYX

The structure of p38 alpha in complex with a triazol inhibitor

• PDB DOI: 10.2210/pdb5XYX/pdb

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


• Deposited: 2017-07-11 Released: 2018-01-17 
• Deposition Author(s): Wang, Y.L., Sun, Y.Z., Cao, R., Liu, D., Li, L., Qi, X.B., Huang, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery.

Wang, Y., Sun, Y., Cao, R., Liu, D., Xie, Y., Li, L., Qi, X., Huang, N.

(2017) J Med Chem 60: 8552-8564

• PubMed: 28945083 
• DOI: 10.1021/acs.jmedchem.7b01075
• Primary Citation of Related Structures:  
  5XYX, 5XYY, 5XYZ


• PubMed Abstract: 
  

To explore novel kinase hinge-binding scaffolds, we carried out structure-based virtual screening against p38α MAPK as a model system. With the assistance of developed kinase-specific structural filters, we identify a novel lead compound that selectively inhibits a panel of kinases with threonine as the gatekeeper residue, including BTK and LCK. These kinases play important roles in lymphocyte activation, which encouraged us to design novel kinase inhibitors as drug candidates for ameliorating inflammatory diseases and cancers. Therefore, we chemically modified our substituted triazole-class lead compound to improve the binding affinity and selectivity via a "minimal decoration" strategy, which resulted in potent and selective kinase inhibitors against LCK (18 nM) and BTK (8 nM). Subsequent crystallographic experiments validated our design. These rationally designed compounds exhibit potent on-target inhibition against BTK in B cells or LCK in T cells, respectively. Our work demonstrates that structure-based virtual screening can be applied to facilitate the development of novel chemical entities in crowded chemical space in the field of kinase inhibitor discovery.

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Organizational Affiliation: 

National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	380	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FTZ	B [auth A]	N-(2-chloro-6-fluorobenzyl)-5-(furan-2-yl)-2H-1,2,4-triazol-3-amine C13 H10 Cl F N4 O AHOHWELPUXLPOF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FTZ	BindingDB:  5XYX	IC50: 1.44e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.15	α = 90
b = 86.13	β = 90
c = 124.77	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-07-11 
• Released Date: 2018-01-17 
Deposition Author(s): Wang, Y.L., Sun, Y.Z., Cao, R., Liu, D., Li, L., Qi, X.B., Huang, N.

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references