4U5J

C-Src in complex with Ruxolitinib

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • 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 s ...

    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.

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RXT
Query on RXT
Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RXTKd: >10000 nM (90) BINDINGDB
RXTIC50: 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 = 42.107α = 79.27
b = 63.228β = 89.27
c = 73.989γ = 90.29
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81272971
National Natural Science Foundation of ChinaChina81372904
National Institutes of Health/National Institute of General Medical SciencesUnited States5R01GM064642

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