8FAU

Masking thiol reactivity with thioamide-based MBPs- carbonic anhydrase II complexed with 4-phenylthiazole-2(3H)-thione

• PDB DOI: https://doi.org/10.2210/pdb8FAU/pdb

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


• Deposited: 2022-11-28 Released: 2023-03-01 
• Deposition Author(s): Kohlbrand, A.J., Seo, H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Masking thiol reactivity with thioamide, thiourea, and thiocarbamate-based MBPs.

Seo, H., Kohlbrand, A.J., Stokes, R.W., Chung, J., Cohen, S.M.

(2023) Chem Commun (Camb) 59: 2283-2286

• PubMed: 36735025 
• DOI: https://doi.org/10.1039/d2cc06596g
• Primary Citation of Related Structures:  
  8FAL, 8FAU


• PubMed Abstract: 
  

  Thioamides, thioureas, and thiocarbamates are introduced as stable, sulfur-based metal-binding pharmacophores (MBPs) for use in metalloenzyme fragment-based drug discovery (mFBDD). MBP reactivity, bioactivity, and structural studies show that these molecules can act as ligands for Zn(II)-dependent metalloenzymes including human carbonic anhydrase II (hCAII) and matrix metalloproteinase-2 (MMP-2).

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. [e-mail].

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: 29.64 kDa 
• Atom Count: 2,397 
• Modelled Residue Count: 256 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y3E (Subject of Investigation/LOI)	B [auth A]	4-phenyl-1,3-thiazole-2(3H)-thione C9 H7 N S2 CYCKHTAVNBPQDB-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SO4	BindingDB:  8FAU	Ki: min: 8.90e+7, max: 3.00e+8 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.144	α = 90
b = 41.316	β = 104.541
c = 71.919	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
APEX	data reduction
APEX	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-01 
Deposition Author(s): Kohlbrand, A.J., Seo, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI149444

Revision History  

• Version 1.0: 2023-03-01
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection