5I2F

Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) with bound sulfamide inhibitor Bio-AMS

• PDB DOI: https://doi.org/10.2210/pdb5I2F/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-08 Released: 2016-06-22 
• Deposition Author(s): Maize, K.M., Finzel, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.175 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

Design, Synthesis, and Characterization of Sulfamide and Sulfamate Nucleotidomimetic Inhibitors of hHint1.

Shah, R., Strom, A., Zhou, A., Maize, K.M., Finzel, B.C., Wagner, C.R.

(2016) ACS Med Chem Lett 7: 780-784

• PubMed: 27563403 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00169
• Primary Citation of Related Structures:  
  5I2E, 5I2F


• PubMed Abstract: 
  

  Hint1 has recently emerged to be an important target of interest due to its involvement in the regulation of a broad range of CNS functions including opioid signaling, tolerance, neuropathic pain, and nicotine dependence. A series of inhibitors were rationally designed, synthesized, and tested for their inhibitory activity against hHint1 using isothermal titration calorimetry (ITC). The studies resulted in the development of the first small-molecule inhibitors of hHint1 with submicromolar binding affinities. A combination of thermodynamic and high-resolution X-ray crystallographic studies provides an insight into the biomolecular recognition of ligands by hHint1. These novel inhibitors have potential utility as molecular probes to better understand the role and function of hHint1 in the CNS.

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Organizational Affiliation: 

Departments of Medicinal Chemistry and Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 28.89 kDa 
• Atom Count: 2,122 
• Modelled Residue Count: 228 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 1	A [auth B], B [auth A]	129	Homo sapiens	Mutation(s): 0  Gene Names: HINT1, HINT EC: 3 (PDB Primary Data), 3.4.22 (UniProt), 3.9.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49773 (Homo sapiens) Explore P49773  Go to UniProtKB:  P49773
PHAROS:  P49773 GTEx:  ENSG00000169567

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BS5	D [auth A]	5'-deoxy-5'-[({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamoyl)amino]adenosine C20 H29 N9 O7 S2 RSZBCKJLQVSFKT-RHCAYAJFSA-N
EDO	C [auth B], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BS5	BindingDB:  5I2F	Kd: 320 (nM) from 1 assay(s)
		IC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.175 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.493	α = 90
b = 46.314	β = 94.44
c = 64.073	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
SCALA	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-22 
Deposition Author(s): Maize, K.M., Finzel, B.C.

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description