2XPA

DISCOVERY OF CELL-ACTIVE PHENYL-IMIDAZOLE PIN1 INHIBITORS BY STRUCTURE-GUIDED FRAGMENT EVOLUTION

PDB DOI: https://doi.org/10.2210/pdb2XPA/pdb

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

Deposited: 2010-08-25 Released: 2011-01-12
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.257
R-Value Work: 0.207
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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

PubMed: 20932746 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 19.37 kDa
Atom Count: 1,315
Modelled Residue Count: 146
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13526
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12P Query on 12P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DODECAETHYLENE GLYCOL C₂₄ H₅₀ O₁₃ WRZXKWFJEFFURH-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
4G5 Query on 4G5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-[(2-amino-2-oxoethyl)(methyl)carbamoyl]-2-phenyl-1H-imidazole-5-carboxylic acid C₁₄ H₁₄ N₄ O₄ IKAWXRIWROBKBL-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
4G5	PDBBind: 2XPA	IC50: 4100 (nM) from 1 assay(s)
4G5	BindingDB: 2XPA	IC50: 4100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.257
R-Value Work: 0.207
R-Value Observed: 0.209
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.367	α = 90
b = 68.367	β = 90
c = 79.351	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-12
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-01-30
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description