9KE5 | pdb_00009ke5

Crystal structure of the PIN1 and fragment 16 complex.

• PDB DOI: https://doi.org/10.2210/pdb9KE5/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-04 Released: 2025-11-12 
• Deposition Author(s): Xiao, Q.J., Wu, T.T., Shu, H.L., Qin, W.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.249 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Fragment-Based Compound Screening Based on PIN1 Crystals

Xiao, Q.J., Wu, T.T., Shu, H.L., Qin, W.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.92 kDa 
• Atom Count: 1,293 
• Modeled Residue Count: 147 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A	163	Homo sapiens	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE8	B [auth A]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
A1EE3 (Subject of Investigation/LOI)	C [auth A]	4-prop-2-ynyl-1,4-thiazinane 1,1-dioxide C7 H11 N O2 S CZBZIZOYSYHBNM-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.249 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.15	α = 90
b = 69.15	β = 90
c = 80.43	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Xiao, Q.J., Wu, T.T., Shu, H.L., Qin, W.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release