Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 19.35 kDa 
• Atom Count: 1311 
• Modelled Residue Count: 147 
• Deposited Residue Count: 167 
• Unique protein chains: 1

3NTP

Human Pin1 complexed with reduced amide inhibitor

• DOI: 10.2210/pdb3NTP/pdb

• Classification: Isomerase/Isomerase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-07-05 Released: 2012-01-04 
• Deposition Author(s): Zhang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.266 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 

Literature

A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

Xu, G.G., Zhang, Y., Mercedes-Camacho, A.Y., Etzkorn, F.A.

(2011) Biochemistry 50: 9545-9550

• PubMed: 21980916 
• DOI: 10.1021/bi201055c
• Primary Citation of Related Structures:  
  3NTP


• PubMed Abstract: 
  

The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.

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Organizational Affiliation: 

Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

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
Find proteins for Q13526 (Homo sapiens) Explore Q13526  Go to UniProtKB:  Q13526
NIH Common Fund Data Resources
PHAROS:  Q13526 GTEx:  ENSG00000127445

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RZD	A	(2R)-2-(acetylamino)-3-[(2S)-2-{[2-(1H-indol-3-yl)ethyl]carbamoyl}pyrrolidin-1-yl]propyl dihydrogen phosphate C20 H29 N4 O6 P FDBFLFSQEGXOJR-APWZRJJASA-N
PE8	A	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RZD	IC50 :  12000   nM  PDBBind
RZD	IC50:  12000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.266 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.847	α = 90
b = 68.847	β = 90
c = 79.782	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-05 
• Released Date: 2012-01-04 
Deposition Author(s): Zhang, Y.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release