3ODK

Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution

• PDB DOI: https://doi.org/10.2210/pdb3ODK/pdb

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


• Deposited: 2010-08-11 Released: 2010-10-27 
• Deposition Author(s): Potter, A., Oldfield, V., Nunns, C., Fromont, C., Ray, S., Northfield, C.J., Bryant, C.J., Scrace, S.F., Robinson, D., Matossova, N., Baker, L., Dokurno, P., Surgenor, A.E., Davis, B.E., Richardson, C.M., Murray, J.B., Moore, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.335 
• R-Value Work: 0.247 
• R-Value Observed: 0.251 

Literature

Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution.

Potter, A., Oldfield, V., Nunns, C., Fromont, C., Ray, S., Northfield, C.J., Bryant, C.J., Scrace, S.F., Robinson, D., Matossova, N., Baker, L., Dokurno, P., Surgenor, A.E., Davis, B., Richardson, C.M., Murray, J.B., Moore, J.D.

(2010) Bioorg Med Chem Lett 20: 6483-6488

• PubMed: 20932746 
• DOI: https://doi.org/10.1016/j.bmcl.2010.09.063
• Primary Citation of Related Structures:  
  2XP3, 2XP4, 2XP5, 2XP6, 2XP7, 2XP8, 2XP9, 2XPA, 2XPB, 3ODK


• PubMed Abstract: 
  

  Pin1 is an emerging oncology target strongly implicated in Ras and ErbB2-mediated tumourigenesis. Pin1 isomerizes bonds linking phospho-serine/threonine moieties to proline enabling it to play a key role in proline-directed kinase signalling. Here we report a novel series of Pin1 inhibitors based on a phenyl imidazole acid core that contains sub-μM inhibitors. Compounds have been identified that block prostate cancer cell growth under conditions where Pin1 is essential.

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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.

Macromolecule Content

• Total Structure Weight: 19.07 kDa 
• Atom Count: 1,260 
• 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): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	B [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
ODK	C [auth A]	3-pyridin-2-yl-1H-pyrazole-5-carboxylic acid C9 H7 N3 O2 SJBWHTBPIJXUFP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ODK	PDBBind:  3ODK	IC50: 7.20e+5 (nM) from 1 assay(s)
	BindingDB:  3ODK	IC50: 7.20e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.335 
• R-Value Work: 0.247 
• R-Value Observed: 0.251 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.048	α = 90
b = 68.048	β = 90
c = 79.567	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: 2010-10-27 
Deposition Author(s): Potter, A., Oldfield, V., Nunns, C., Fromont, C., Ray, S., Northfield, C.J., Bryant, C.J., Scrace, S.F., Robinson, D., Matossova, N., Baker, L., Dokurno, P., Surgenor, A.E., Davis, B.E., Richardson, C.M., Murray, J.B., Moore, J.D.

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations