8OO8 | pdb_00008oo8

Three-Dimensional Structure of Human Carbonic Anhydrase II in Complex with a Covalent Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.215 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8OO8

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Targeted anticancer pre-vinylsulfone covalent inhibitors of carbonic anhydrase IX.

Vaskevicius, A.Baronas, D.Leitans, J.Kvietkauskaite, A.Ruksenaite, A.Manakova, E.Toleikis, Z.Kaupinis, A.Kazaks, A.Gedgaudas, M.Mickeviciute, A.Juozapaitiene, V.Schioth, H.B.Jaudzems, K.Valius, M.Tars, K.Grazulis, S.Meyer-Almes, F.J.Matuliene, J.Zubriene, A.Dudutiene, V.Matulis, D.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.101401
  • Primary Citation Related Structures: 
    8OO8, 8S4F, 9FLF

  • PubMed Abstract: 

    We designed novel pre-drug compounds that transform into an active form that covalently modifies particular His residue in the active site, a difficult task to achieve, and applied to carbonic anhydrase (CAIX), a transmembrane protein, highly overexpressed in hypoxic solid tumors, important for cancer cell survival and proliferation because it acidifies tumor microenvironment helping invasion and metastases processes. The designed compounds have several functionalities: (1) primary sulfonamide group recognizing carbonic anhydrases (CA), (2) high-affinity moieties specifically recognizing CAIX among all CA isozymes, and (3) forming a covalent bond with the His64 residue. Such targeted covalent compounds possess both high initial affinity and selectivity for the disease target protein followed by complete irreversible inactivation of the protein via covalent modification. Our designed prodrug candidates bearing moderately active pre-vinylsulfone esters or weakly active carbamates optimized for mild covalent modification activity to avoid toxic non-specific modifications and selectively target CAIX. The lead inhibitors reached 2 pM affinity, the highest among known CAIX inhibitors. The strategy could be used for any disease drug target protein bearing a His residue in the vicinity of the active site.


  • Organizational Affiliation
    • Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.

Macromolecule Content 

  • Total Structure Weight: 29.65 kDa 
  • Atom Count: 2,411 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 259 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2259Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VV8
(Subject of Investigation/LOI)

Query on VV8



Download:Ideal Coordinates CCD File
C [auth A]3-(cyclooctylamino)-4-ethylsulfonyl-2,5,6-tris(fluoranyl)benzenesulfonamide
C16 H23 F3 N2 O4 S2
JATZJQNOFRECGS-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.215 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.45α = 90
b = 41.57β = 104.4
c = 72.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling

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: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary
  • Version 1.2: 2025-01-22
    Changes: Database references