7Q0D | pdb_00007q0d

Human carbonic anhydrase I in complex with Methyl 2-(benzenesulfonyl)-4-chloro-5-sulfamoylbenzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 
    0.158 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.131 (Depositor) 
  • R-Value Observed: 
    0.134 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Q0D

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Methyl 2-Halo-4-Substituted-5-Sulfamoyl-Benzoates as High Affinity and Selective Inhibitors of Carbonic Anhydrase IX.

Zaksauskas, A.Capkauskaite, E.Paketuryte-Latve, V.Smirnov, A.Leitans, J.Kazaks, A.Dvinskis, E.Stancaitis, L.Mickeviciute, A.Jachno, J.Jezepcikas, L.Linkuviene, V.Sakalauskas, A.Manakova, E.Grazulis, S.Matuliene, J.Tars, K.Matulis, D.

(2021) Int J Mol Sci 23

  • DOI: https://doi.org/10.3390/ijms23010130
  • Primary Citation Related Structures: 
    7POM, 7PP9, 7PUU, 7PUV, 7PUW, 7Q0C, 7Q0D, 7Q0E

  • PubMed Abstract: 

    Among the twelve catalytically active carbonic anhydrase isozymes present in the human body, the CAIX is highly overexpressed in various solid tumors. The enzyme acidifies the tumor microenvironment enabling invasion and metastatic processes. Therefore, many attempts have been made to design chemical compounds that would exhibit high affinity and selective binding to CAIX over the remaining eleven catalytically active CA isozymes to limit undesired side effects. It has been postulated that such drugs may have anticancer properties and could be used in tumor treatment. Here we have designed a series of compounds, methyl 5-sulfamoyl-benzoates, which bear a primary sulfonamide group, a well-known marker of CA inhibitors, and determined their affinities for all twelve CA isozymes. Variations of substituents on the benzenesulfonamide ring led to compound 4b , which exhibited an extremely high observed binding affinity to CAIX; the K d was 0.12 nM. The intrinsic dissociation constant, where the binding-linked protonation reactions have been subtracted, reached 0.08 pM. The compound also exhibited more than 100-fold selectivity over the remaining CA isozymes. The X-ray crystallographic structure of compound 3b bound to CAIX showed the structural position, while several structures of compounds bound to other CA isozymes showed structural reasons for compound selectivity towards CAIX. Since this series of compounds possess physicochemical properties suitable for drugs, they may be developed for anticancer therapeutic purposes.


  • Organizational Affiliation
    • Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.

Macromolecule Content 

  • Total Structure Weight: 60.85 kDa 
  • Atom Count: 5,464 
  • Modeled Residue Count: 516 
  • Deposited Residue Count: 522 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 1
A, B
261Homo sapiensMutation(s): 0 
Gene Names: CA1
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens)
Explore P00915 
Go to UniProtKB:  P00915
PHAROS:  P00915
GTEx:  ENSG00000133742 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00915
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
84Z
(Subject of Investigation/LOI)

Query on 84Z



Download:Ideal Coordinates CCD File
D [auth A],
S [auth B]
methyl 4-chloranyl-2-(phenylsulfonyl)-5-sulfamoyl-benzoate
C14 H12 Cl N O6 S2
IGXGTYUIRLTUTM-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AA [auth B]
J [auth A]
K [auth A]
L [auth A]
T [auth B]
AA [auth B],
J [auth A],
K [auth A],
L [auth A],
T [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



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

Query on EDO



Download:Ideal Coordinates CCD File
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
EA [auth B]
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
HA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
V [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
ACT BindingDB:  7Q0D Ki: 1.08e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free:  0.158 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.131 (Depositor) 
  • R-Value Observed: 0.134 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.039α = 90
b = 73.235β = 90
c = 120.473γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Cootmodel building

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: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2025-10-01
    Changes: Derived calculations, Structure summary