Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66066.02 
• Atom Count: 4336 
• Residue Count: 572 
• Unique protein chains: 1

4U5J

C-Src in complex with Ruxolitinib

• DOI: 10.2210/pdb4U5J/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Gallus gallus
• Expression System: Escherichia coli #1/H766


• Deposited: 2014-07-25 Released: 2014-09-17 
• Deposition Author(s): Chen, Y., Duan, Y., Chen, L.
• Funding Organization(s): National Natural Science Foundation of China; National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 

Literature

c-Src Binds to the Cancer Drug Ruxolitinib with an Active Conformation

Duan, Y., Chen, L., Chen, Y., Fan, X.G.

(2014) Plos One 9: e106225-e106225

• PubMed: 25197973 
• DOI: 10.1371/journal.pone.0106225


• PubMed Abstract: 
  

The cancer drug Ruxolitinib is a potent janus kinase inhibitor approved for the treatment of the myeloproliferative neoplasms. In addition, Ruxolitinib has weak inhibitory activity against a panel of other kinases, including Src kinase. There is no structural information of Ruxolitinib binding to any kinase. In this paper, we determined the crystal structure of c-Src kinase domain in complex of Ruxolitinib at a resolution of 2.26 Å. C-Src kinase domain adopts the DFG-in active conformation upon Ruxolitinib binding, indicating Ruxolitinib is a type I inhibitor for c-Src. Ruxolitinib forms two hydrogen bonds with Met341, a water-mediated hydrogen bond with Thr338, and a number of van der Waals contacts with c-Src. Ruxolitinib was then docked into the ligand-binding pocket of a previously solved JAK1 structure. From the docking result, Ruxolitinib also binds JAK1 as a type I inhibitor, with more interactions and a higher shape complementarity with the ligand-binding pocket of JAK1 compared to that of c-Src. Since Ruxolitinib is a relatively small inhibitor and there is sizeable cavity between Ruxolitinib and c-Src ligand-binding pocket, we propose to modify Ruxolitinib to develop more potent inhibitors to c-Src.

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Organizational Affiliation: 

Department of Infectious Diseases & Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan, China.,Department of Infectious Diseases & Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan, China; Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 0  Gene Names: SRC EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus) Go to Gene View: SRC Go to UniProtKB:  P00523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
RXT	A, B	(3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile Ruxolitinib C17 H18 N6 HFNKQEVNSGCOJV-OAHLLOKOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RXT	Kd: >10000 nM (90) BINDINGDB
RXT	IC50: 2920 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.107	α = 79.27
b = 63.228	β = 89.27
c = 73.989	γ = 90.29

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-07-25 
• Released Date: 2014-09-17 
• Deposition Author(s): Chen, Y., Duan, Y., Chen, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81272971
National Natural Science Foundation of China	China	81372904
National Institutes of Health/National Institute of General Medical Sciences	United States	5R01GM064642

Revision History 

• Version 1.0: 2014-09-17
  Type: Initial release
• Version 1.1: 2017-10-18
  Type: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary