6VAJ

Crystal Structure Analysis of human PIN1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.5 of the entry. See complete history


Literature

Sulfopin is a covalent inhibitor of Pin1 that blocks Myc-driven tumors in vivo.

Dubiella, C.Pinch, B.J.Koikawa, K.Zaidman, D.Poon, E.Manz, T.D.Nabet, B.He, S.Resnick, E.Rogel, A.Langer, E.M.Daniel, C.J.Seo, H.S.Chen, Y.Adelmant, G.Sharifzadeh, S.Ficarro, S.B.Jamin, Y.Martins da Costa, B.Zimmerman, M.W.Lian, X.Kibe, S.Kozono, S.Doctor, Z.M.Browne, C.M.Yang, A.Stoler-Barak, L.Shah, R.B.Vangos, N.E.Geffken, E.A.Oren, R.Koide, E.Sidi, S.Shulman, Z.Wang, C.Marto, J.A.Dhe-Paganon, S.Look, T.Zhou, X.Z.Lu, K.P.Sears, R.C.Chesler, L.Gray, N.S.London, N.

(2021) Nat Chem Biol 17: 954-963

  • DOI: https://doi.org/10.1038/s41589-021-00786-7
  • Primary Citation of Related Structures:  
    6VAJ

  • PubMed Abstract: 

    The peptidyl-prolyl isomerase, Pin1, is exploited in cancer to activate oncogenes and inactivate tumor suppressors. However, despite considerable efforts, Pin1 has remained an elusive drug target. Here, we screened an electrophilic fragment library to identify covalent inhibitors targeting Pin1's active site Cys113, leading to the development of Sulfopin, a nanomolar Pin1 inhibitor. Sulfopin is highly selective, as validated by two independent chemoproteomics methods, achieves potent cellular and in vivo target engagement and phenocopies Pin1 genetic knockout. Pin1 inhibition had only a modest effect on cancer cell line viability. Nevertheless, Sulfopin induced downregulation of c-Myc target genes, reduced tumor progression and conferred survival benefit in murine and zebrafish models of MYCN-driven neuroblastoma, and in a murine model of pancreatic cancer. Our results demonstrate that Sulfopin is a chemical probe suitable for assessment of Pin1-dependent pharmacology in cells and in vivo, and that Pin1 warrants further investigation as a potential cancer drug target.


  • Organizational Affiliation

    Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1178Homo sapiensMutation(s): 2 
Gene Names: PIN1
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13526 (Homo sapiens)
Explore Q13526 
Go to UniProtKB:  Q13526
PHAROS:  Q13526
GTEx:  ENSG00000127445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13526
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QT7
Query on QT7

Download Ideal Coordinates CCD File 
B [auth A]2-chloro-N-(2,2-dimethylpropyl)-N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetamide
C11 H20 Cl N O3 S
NMHVAHHYKGXBMY-SECBINFHSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.96α = 90
b = 48.96β = 90
c = 137.04γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references
  • Version 1.3: 2021-09-08
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary