7SV1 | pdb_00007sv1

Carbonic Anhydrase IX-mimic Complexed with 3-((2-((Naphthalen-2-ylmethyl)(4-sulfamoylphenethyl)amino)-2-oxoethyl)(phenethyl)amino)propanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7SV1

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

The three-tails approach as a new strategy to improve selectivity of action of sulphonamide inhibitors against tumour-associated carbonic anhydrase IX and XII.

Bonardi, A.Bua, S.Combs, J.Lomelino, C.Andring, J.Osman, S.M.Toti, A.Di Cesare Mannelli, L.Gratteri, P.Ghelardini, C.McKenna, R.Nocentini, A.Supuran, C.T.

(2022) J Enzyme Inhib Med Chem 37: 930-939

  • DOI: https://doi.org/10.1080/14756366.2022.2053526
  • Primary Citation Related Structures: 
    7SUW, 7SUY, 7SV1, 7SV8

  • PubMed Abstract: 

    Human (h) carbonic anhydrase (CAs, EC 4.2.1.1) isoforms IX and XII were recently confirmed as anticancer targets against solid hypoxic tumours. The "three-tails approach" has been proposed as an extension of the forerunner "tail" and "dual-tail approach" to fully exploit the amino acid differences at the medium/outer active site rims among different hCAs and to obtain more isoform-selective inhibitors. Many three-tailed inhibitors (TTIs) showed higher selectivity against the tumour-associated isoforms hCA IX and XII with respect to the off-targets hCA I and II. X-ray crystallography studies were performed to investigate the binding mode of four TTIs in complex with a hCA IX mimic. The ability of the most potent and selective TTIs to reduce in vitro the viability of colon cancer (HT29), prostate adenocarcinoma (PC3), and breast cancer (ZR75-1) cell lines was evaluated in normoxic (21% O 2 ) and hypoxic (3% O 2 ) conditions demonstrating relevant anti-proliferative effects.


  • Organizational Affiliation
    • Department NEUROFARBA - Pharmaceutical and Nutraceutical Section, University of Firenze, Florence, Italy.

Macromolecule Content 

  • Total Structure Weight: 29.56 kDa 
  • Atom Count: 2,248 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 257 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2257Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U6V
(Subject of Investigation/LOI)

Query on U6V



Download:Ideal Coordinates CCD File
D [auth A]N~2~-(3-aminopropyl)-N-[(4-fluorophenyl)methyl]-N~2~-(2-phenylethyl)-N-[2-(4-sulfamoylphenyl)ethyl]glycinamide
C28 H35 F N4 O3 S
PTOFZDQATQXAPS-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
B [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN

Query on ZN



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.927α = 90
b = 41.43β = 103.79
c = 71.985γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

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: 2022-04-06
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description