3KAF

Structure-guided design of alpha-amino acid-derived Pin1 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3KAF/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-10-19 Released: 2009-12-22 
• Deposition Author(s): Baker, L.M., Dokurno, P., Robinson, D.A., Surgenor, A.E., Murray, J.B., Potter, A.J., Moore, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.312 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Structure-guided design of alpha-amino acid-derived Pin1 inhibitors

Potter, A.J., Ray, S., Gueritz, L., Nunns, C.L., Bryant, C.J., Scrace, S.F., Matassova, N., Baker, L.M., Dokurno, P., Robinson, D.A., Surgenor, A.E., Davis, B., Murray, J.B., Richardson, C.M., Moore, J.D.

(2010) Bioorg Med Chem Lett 20: 586-590

• PubMed: 19969456 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.090
• Primary Citation of Related Structures:  
  3KAB, 3KAC, 3KAD, 3KAF, 3KAG, 3KAH, 3KAI, 3KCE


• PubMed Abstract: 
  

  The peptidyl prolyl cis/trans isomerase Pin1 is a promising molecular target for anti-cancer therapeutics. Here we report the structure-guided evolution of an indole 2-carboxylic acid fragment hit into a series of alpha-benzimidazolyl-substituted amino acids. Examples inhibited Pin1 activity with IC(50) <100nM, but were inactive on cells. Replacement of the benzimidazole ring with a naphthyl group resulted in a 10-50-fold loss in ligand potency, but these examples downregulated biomarkers of Pin1 activity and blocked proliferation of PC3 cells.

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Organizational Affiliation: 

Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 18.83 kDa 
• Atom Count: 1,226 
• Modelled Residue Count: 145 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A	167	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
4D9	B [auth A]	3-(1H-benzimidazol-2-yl)-N-(1-benzothiophen-2-ylcarbonyl)-D-alanine C19 H15 N3 O3 S OEMQUBXYMQNIGH-CQSZACIVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4D9	BindingDB:  3KAF	Kd: 1.00e+4 (nM) from 1 assay(s)
		IC50: 830 (nM) from 1 assay(s)
	PDBBind:  3KAF	IC50: 830 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.312 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.937	α = 90
b = 67.937	β = 90
c = 79.247	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Baker, L.M., Dokurno, P., Robinson, D.A., Surgenor, A.E., Murray, J.B., Potter, A.J., Moore, J.D.

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description