3IKG

Structure-Based Design of Novel PIN1 Inhibitors (I)

• PDB DOI: https://doi.org/10.2210/pdb3IKG/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-08-05 Released: 2009-09-22 
• Deposition Author(s): Parge, H., Ferre, R.A., Greasley, S., Matthews, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Structure-based design of novel human Pin1 inhibitors (I).

Guo, C., Hou, X., Dong, L., Dagostino, E., Greasley, S., Ferre, R., Marakovits, J., Johnson, M.C., Matthews, D., Mroczkowski, B., Parge, H., Vanarsdale, T., Popoff, I., Piraino, J., Margosiak, S., Thomson, J., Los, G., Murray, B.W.

(2009) Bioorg Med Chem Lett 19: 5613-5616

• PubMed: 19729306 
• DOI: https://doi.org/10.1016/j.bmcl.2009.08.034
• Primary Citation of Related Structures:  
  3IK8, 3IKD, 3IKG


• PubMed Abstract: 
  

  Pin1 is a member of the cis-trans peptidyl-prolyl isomerase family with potential anti-cancer therapeutic value. Here we report structure-based de novo design and optimization of novel Pin1 inhibitors. Without a viable lead from internal screenings, we designed a series of novel Pin1 inhibitors by interrogating and exploring a protein crystal structure of Pin1. The ligand efficiency of the initial concept molecule was optimized with integrated SBDD and parallel chemistry approaches, resulting in a more attractive lead series.

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Organizational Affiliation: 

Pfizer Global Research and Development, 10770 Science Center Drive, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.13 kDa 
• Atom Count: 2,002 
• Modelled Residue Count: 226 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A, B	123	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J8Z	C [auth A], D [auth B]	(2R)-2-[(1-benzothiophen-2-ylcarbonyl)amino]-3-(3-methylphenyl)propyl phosphate C19 H18 N O5 P S VJUQXEZAYUVHJF-MRXNPFEDSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
J8Z	PDBBind:  3IKG	Ki: 57 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.255	α = 90
b = 36.53	β = 100.4
c = 51.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELX	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Parge, H., Ferre, R.A., Greasley, S., Matthews, D.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-03-30
  Changes: Other
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description