5DH3

Crystal structure of MST2 in complex with XMU-MP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Pharmacological targeting of kinases MST1 and MST2 augments tissue repair and regeneration

Fan, F.He, Z.Kong, L.L.Chen, Q.Yuan, Q.Zhang, S.Ye, J.Liu, H.Sun, X.Geng, J.Yuan, L.Hong, L.Xiao, C.Zhang, W.Sun, X.Li, Y.Wang, P.Huang, L.Wu, X.Ji, Z.Wu, Q.Xia, N.S.Gray, N.S.Chen, L.Yun, C.H.Deng, X.Zhou, D.

(2016) Sci Transl Med 8: 352ra108-352ra108

  • DOI: 10.1126/scitranslmed.aaf2304
  • Primary Citation of Related Structures:  
    5DH3

  • PubMed Abstract: 
  • Tissue repair and regenerative medicine address the important medical needs to replace damaged tissue with functional tissue. Most regenerative medicine strategies have focused on delivering biomaterials and cells, yet there is the untapped potential for ...

    Tissue repair and regenerative medicine address the important medical needs to replace damaged tissue with functional tissue. Most regenerative medicine strategies have focused on delivering biomaterials and cells, yet there is the untapped potential for drug-induced regeneration with good specificity and safety profiles. The Hippo pathway is a key regulator of organ size and regeneration by inhibiting cell proliferation and promoting apoptosis. Kinases MST1 and MST2 (MST1/2), the mammalian Hippo orthologs, are central components of this pathway and are, therefore, strong target candidates for pharmacologically induced tissue regeneration. We report the discovery of a reversible and selective MST1/2 inhibitor, 4-((5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino)benzenesulfonamide (XMU-MP-1), using an enzyme-linked immunosorbent assay-based high-throughput biochemical assay. The cocrystal structure and the structure-activity relationship confirmed that XMU-MP-1 is on-target to MST1/2. XMU-MP-1 blocked MST1/2 kinase activities, thereby activating the downstream effector Yes-associated protein and promoting cell growth. XMU-MP-1 displayed excellent in vivo pharmacokinetics and was able to augment mouse intestinal repair, as well as liver repair and regeneration, in both acute and chronic liver injury mouse models at a dose of 1 to 3 mg/kg via intraperitoneal injection. XMU-MP-1 treatment exhibited substantially greater repopulation rate of human hepatocytes in the Fah-deficient mouse model than in the vehicle-treated control, indicating that XMU-MP-1 treatment might facilitate human liver regeneration. Thus, the pharmacological modulation of MST1/2 kinase activities provides a novel approach to potentiate tissue repair and regeneration, with XMU-MP-1 as the first lead for the development of targeted regenerative therapeutics.


    Organizational Affiliation

    State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China. State-Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, Xiamen University, Xiamen, Fujian 361102, China. dwzhou@xmu.edu.cn xmdeng@xmu.edu.cn yunch@hsc.pku.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 3 AB315Homo sapiensMutation(s): 0 
Gene Names: STK3KRS1MST2
EC: 2.7.11.1
Find proteins for Q13188 (Homo sapiens)
Explore Q13188 
Go to UniProtKB:  Q13188
NIH Common Fund Data Resources
PHAROS:  Q13188
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5BS
Query on 5BS

Download Ideal Coordinates CCD File 
A, B
4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide
C17 H16 N6 O3 S2
YRDHKIFCGOZTGD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A,BL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5BSIC50:  38.099998474121094   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.871α = 90
b = 98.462β = 90
c = 166.771γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data processing
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-29 
  • Released Date: 2016-08-31 
  • Deposition Author(s): Kong, L.L., Yun, C.H.

Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2012CB917202
National Science Foundation of ChinaChina31270769

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Derived calculations