9INR

Crystal structure of PIN1 in complex with inhibitor C3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 

Starting Model: experimental
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Literature

Re-Evaluating PIN1 as a Therapeutic Target in Oncology Using Neutral Inhibitors and PROTACs.

Liu, C.Chen, Z.Chen, T.Song, H.Shen, J.Yuan, X.Xia, S.Liu, Q.Chen, Q.Tian, Q.Meng, X.Han, Z.Dong, X.Yang, Y.Cai, L.Cheng, X.Jia, Y.Liu, G.Li, J.Ge, J.Dou, D.

(2024) J Med Chem 67: 15780-15795

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01412
  • Primary Citation of Related Structures:  
    9INR

  • PubMed Abstract: 

    Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1) has emerged as a promising therapeutic target for cancer treatment. However, the current PIN1 inhibitors have shown limited efficacy in animal models, leaving the question of whether PIN1 is a proper oncologic target still unanswered. By screening a 1 trillion DNA-encoded library (DEL), we identified novel nonacidic compounds. Among resynthesized DEL compounds, DEL1067 - 56 - 469 ( A0 ) is the most potent one (KD = 430 nM, IC 50 = 420 nM). Further optimization of A0 resulted in compound C10 with much improved potency (KD = 25 nM, IC 50 = 150 nM). As an alternative approach, C10 was then converted into proteolysis targeting chimeras (PROTACs) in order to achieve deeper downregulation of the PIN1 protein in cancer cell lines. Unfortunately, neither PIN1 inhibitors nor PIN1 PROTACs demonstrated meaningful antiproliferation activity. In addition, siRNA knock-down experiments provided unfavorable evidence of PIN1 as an oncologic target. Our findings highlight the complexity of targeting PIN1 for cancer therapy.


  • Organizational Affiliation

    HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
A, B
163Homo sapiensMutation(s): 0 
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
PE3 (Subject of Investigation/LOI)
Query on PE3

Download Ideal Coordinates CCD File 
G [auth B]3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
A1D9K (Subject of Investigation/LOI)
Query on A1D9K

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
~{N}-[(2~{S})-3-[1-[4-(4-cyanophenyl)phenyl]-1,2,3-triazol-4-yl]-1-[(3-oxidanylcyclobutyl)amino]-1-oxidanylidene-propan-2-yl]-1-phenyl-cyclopropane-1-carboxamide
C32 H30 N6 O3
LVSHHZHUWFBHGX-OYFGVDPJSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.59α = 90
b = 176.64β = 90
c = 42.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-09-25 
  • Deposition Author(s): Zhang, L.Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release