7K6T | pdb_00007k6t

Carbonic Anhydrase IX mimic complexed with 4-(2-(3-phenylureido)ethylsulfonamido)benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb7K6T/pdb

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


• Deposited: 2020-09-21 Released: 2020-12-23 
• Deposition Author(s): Andring, J.T., Singh, S., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Handling drug-target selectivity: A study on ureido containing Carbonic Anhydrase inhibitors.

Akgul, O., Singh, S., Andring, J.T., McKenna, R., Selleri, S., Carta, F., Angeli, A., Supuran, C.T.

(2021) Eur J Med Chem 212: 113035-113035

• PubMed: 33303238 
• DOI: https://doi.org/10.1016/j.ejmech.2020.113035
• Primary Citation Related Structures: 
  7K6I, 7K6J, 7K6K, 7K6L, 7K6T, 7K6U, 7K6X, 7K6Z


• PubMed Abstract: 
  

  Here we report the synthesis of a series of taurine substituted sulfonamide derivatives 1-29 having the ureido moiety installed at the tail section as selective inhibitors of the tumor associated human (h) Carbonic Anhydrase (CA; EC 4.2.1.1) IX and XII. The series was deeply investigated for their kinetic features which demonstrated a strong dependence on the ureido moiety. High resolution X-ray crystallographic investigation on selected ligand adducts complexed with hCA II and hCA IX-mimic revealed a strong correlation between the ureido moiety and the amino acid residues Q92 and Q67 in both the hCA II and hCA IX-mimic, contributing to highly stabilized ligand-protein complex.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, 35100, Bornova, İzmir, Turkey. Electronic address: [e-mail].
Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
Università Degli Studi di Firenze, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy.
Università Degli Studi di Firenze, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.76 kDa 
• Atom Count: 2,234 
• Modeled Residue Count: 257 
• 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): 7  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
VYV (Subject of Investigation/LOI)	C [auth A]	4-[({2-[(phenylcarbamoyl)amino]ethyl}sulfonyl)amino]benzene-1-sulfonamide C15 H18 N4 O5 S2 JWGFBEXNOWIWRP-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.993	α = 90
b = 74.257	β = 90
c = 76.707	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Andring, J.T., Singh, S., McKenna, R.

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description