6UGO

Human Carbonic Anhydrase IX-mimic complexed with SB4-205


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

"A Sweet Combination": Developing Saccharin and Acesulfame K Structures for Selectively Targeting the Tumor-Associated Carbonic Anhydrases IX and XII.

Bua, S.Lomelino, C.Murray, A.B.Osman, S.M.ALOthman, Z.A.Bozdag, M.Abdel-Aziz, H.A.Eldehna, W.M.McKenna, R.Nocentini, A.Supuran, C.T.

(2020) J Med Chem 63: 321-333

  • DOI: 10.1021/acs.jmedchem.9b01669
  • Primary Citation of Related Structures:  
    6U4Q, 6U4T, 6UGN, 6UGO, 6UGP, 6UGQ, 6UGR, 6UGZ, 6UH0

  • PubMed Abstract: 
  • The sweeteners saccharin ( SAC ) and acesulfame K ( ACE ) recently entered the topic of anticancer human carbonic anhydrase (CA, EC 4.2.1.1) inhibitors, as they showed to selectively inhibit the tumor-associated CAs IX/XII over ubiquitous CAs ...

    The sweeteners saccharin ( SAC ) and acesulfame K ( ACE ) recently entered the topic of anticancer human carbonic anhydrase (CA, EC 4.2.1.1) inhibitors, as they showed to selectively inhibit the tumor-associated CAs IX/XII over ubiquitous CAs. A drug design strategy is here reported, which took SAC and ACE as leads and produced a series of 2 H -benzo[ e ][1,2,4]thiadiazin-3(4 H )-one-1,1-dioxides ( BTD ). Many derivatives showed greater potency ( K I s-CA IX 19.1-408.5 nM) and selectivity (II/IX SI 2-76) than the leads ( K I s-CA IX 103, 2400 nM; II/IX-SI 56, >4) against CA IX/XII over off-target isoforms. A thorough X-ray crystallographic study depicted their binding mode to both CA II and IX-mimic. The most representative BTDs were characterized in vitro for their antitumor activity against A549, PC-3, and HCT-116 cancer cell lines both in normoxia and hypoxia. The two most effective compounds were assayed for their effect on several apoptosis markers, identifying promising leads for the development of new anticancer drugs.


    Organizational Affiliation

    Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , via Ugo Schiff 6 , 50019 Sesto Fiorentino, Florence , Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase IX-mimicA257Homo sapiensMutation(s): 7 
Gene Names: CA2
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q77 (Subject of Investigation/LOI)
Query on Q77

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]5,7-dimethyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione
C9 H10 N2 O3 S
OLDBDPLNTRFOOO-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
F [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.147α = 90
b = 41.362β = 103.97
c = 72.047γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references