3ACL

Crystal Structure of Human Pirin in complex with Triphenyl Compound

• PDB DOI: https://doi.org/10.2210/pdb3ACL/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-01-05 Released: 2010-08-18 
• Deposition Author(s): Okumura, H., Miyazaki, I., Simizu, S., Osada, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

A small-molecule inhibitor shows that pirin regulates migration of melanoma cells

Miyazaki, I., Simizu, S., Okumura, H., Takagi, S., Osada, H.

(2010) Nat Chem Biol 6: 667-673

• PubMed: 20711196 
• DOI: https://doi.org/10.1038/nchembio.423
• Primary Citation of Related Structures:  
  3ACL


• PubMed Abstract: 
  

  The discovery of small molecules that bind to a specific target and disrupt the function of proteins is an important step in chemical biology, especially for poorly characterized proteins. Human pirin is a nuclear protein of unknown function that is widely expressed in punctate subnuclear structures in human tissues. Here, we report the discovery of a small molecule that binds to pirin. We determined how the small molecule bound to pirin by solving the cocrystal structure. Either knockdown of pirin or treatment with the small molecule inhibited melanoma cell migration. Thus, inhibition of pirin by the small molecule has led to a greater understanding of the function of pirin and represents a new method of studying pirin-mediated signaling pathways.

---

Organizational Affiliation: 

Chemical Library Validation Team, Chemical Biology Core Facility, Chemical Biology Department, RIKEN Advanced Science Institute, Wako, Saitama, Japan.

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: 33.44 kDa 
• Atom Count: 2,410 
• Modelled Residue Count: 288 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pirin	A	296	Homo sapiens	Mutation(s): 0  Gene Names: PIR
UniProt & NIH Common Fund Data Resources
Find proteins for O00625 (Homo sapiens) Explore O00625  Go to UniProtKB:  O00625
PHAROS:  O00625 GTEx:  ENSG00000087842

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3F1	C [auth A]	N-{[4-(benzyloxy)phenyl](methyl)-lambda~4~-sulfanylidene}-4-methylbenzenesulfonamide C21 H21 N O3 S2 IMUPOWQOXOCVBN-AREMUKBSSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3F1	Binding MOAD:  3ACL	Kd: 600 (nM) from 1 assay(s)
	PDBBind:  3ACL	Kd: 600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.343	α = 90
b = 67.415	β = 90
c = 107.785	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Okumura, H., Miyazaki, I., Simizu, S., Osada, H.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description