8DPC | pdb_00008dpc

Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural Characterization of Thiadiazolesulfonamide Inhibitors Bound to Neisseria gonorrhoeae alpha-Carbonic Anhydrase.

Marapaka, A.K.Nocentini, A.Youse, M.S.An, W.Holly, K.J.Das, C.Yadav, R.Seleem, M.N.Supuran, C.T.Flaherty, D.P.

(2023) ACS Med Chem Lett 14: 103-109

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00471
  • Primary Citation Related Structures: 
    8DPC, 8DQF, 8DR2, 8DRB, 8DYQ

  • PubMed Abstract: 

    Drug-resistant Neisseria gonorrhoeae is a critical threat to public health, and bacterial carbonic anhydrases expressed by N. gonorrhoeae are potential new therapeutic targets to combat this pathogen. To further expand upon our recent reports of bacterial carbonic anhydrase inhibitors for the treatment of N. gonorrhoeae , our team has solved ligand-bound crystal structures of the FDA-approved carbonic anhydrase inhibitor acetazolamide, along with three analogs, in complex with the essential α-carbonic anhydrase isoform from N. gonorrhoeae . The structural data for the analogs presented bound to N. gonorrhoeae α-carbonic anhydrase supports the observed structure-activity relationship for in vitro inhibition with this scaffold against the enzyme. Moreover, the ligand-bound structures indicate differences in binding poses compared to those traditionally observed with the close human ortholog carbonic anhydrase II. These results present key differences in inhibitor binding between N. gonorrhoeae α-carbonic anhydrase and the human carbonic anhydrase II isoform.


  • Organizational Affiliation
    • Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana47907, United States.

Macromolecule Content 

  • Total Structure Weight: 110.58 kDa 
  • Atom Count: 7,145 
  • Modeled Residue Count: 888 
  • Deposited Residue Count: 972 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydraseA,
B [auth C],
C [auth E],
D [auth G]
243Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: cah
EC: 4.2.1.1
UniProt
Find proteins for Q50940 (Neisseria gonorrhoeae)
Explore Q50940 
Go to UniProtKB:  Q50940
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50940
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth C]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth C],
L [auth C],
M [auth C],
O [auth E],
P [auth E],
R [auth G],
S [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
J [auth C],
N [auth E],
Q [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.158α = 90
b = 122.76β = 116.87
c = 78.67γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI148523

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary