8CO0 | pdb_00008co0

Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.212 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Atropo/Tropo Flexibility: A Tool for Design and Synthesis of Self-Adaptable Inhibitors of Carbonic Anhydrases and Their Antiproliferative Effect.

Ivanova, J.N.Nocentini, A.Tars, K.Leita Ns, J.N.Dvinskis, E.Kazaks, A.Domraceva, I.Supuran, C.T.Zalubovskis, R.

(2023) J Med Chem 66: 5703-5718

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00007
  • Primary Citation Related Structures: 
    8CO0, 8CO3

  • PubMed Abstract: 

    Here, we report for the first time a series of sulfonamide derivatives with scaffolds bearing flexible moieties, namely, rotamers or tropoisomers capable of adapting their geometry in the active center of enzymes thus being effective and selective carbonic anhydrase (CAs, EC 4.2.1.1) enzyme inhibitors. All compounds exhibited effective in vitro inhibition activity toward the main hCA isoforms related to cancer (i.e., hCA II, hCA IX, and hCA XII with K I values in the low nanomolar range). Three selected compounds showed a great cytotoxic effect on cancer cell lines ex vivo. X-ray crystallographic experiments assessed the binding modes of compound 35 with active centers of hCA IX and hCA XII.


  • Organizational Affiliation
    • Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia.

Macromolecule Content 

  • Total Structure Weight: 114.9 kDa 
  • Atom Count: 8,493 
  • Modeled Residue Count: 1,004 
  • Deposited Residue Count: 1,028 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 9A,
B [auth C],
C [auth E],
D [auth G]
257Homo sapiensMutation(s): 2 
Gene Names: CA9G250MN
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16790 (Homo sapiens)
Explore Q16790 
Go to UniProtKB:  Q16790
PHAROS:  Q16790
GTEx:  ENSG00000107159 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16790
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V8O
(Subject of Investigation/LOI)

Query on V8O



Download:Ideal Coordinates CCD File
F [auth A],
I [auth C],
L [auth E],
O [auth G]
5-(5-methyl-6-quinolin-5-yl-pyridin-3-yl)thiophene-2-sulfonamide
C19 H15 N3 O2 S2
FBQWYQWUVBYRAC-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
J [auth C],
M [auth E],
P [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.212 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.951α = 90
b = 152.951β = 90
c = 172.438γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary