7K6U

Carbonic Anhydrase IX mimic complexed with 4-(2-(3-(4-methylphenyl)ureido)ethylsulfonamido)benzenesulfonamide

PDB DOI: https://doi.org/10.2210/pdb7K6U/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-09-21 Released: 2020-12-23
Deposition Author(s): Andring, J.T., Singh, S., McKenna, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.196
R-Value Work: 0.178
R-Value Observed: 0.179

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Handling drug-target selectivity: A study on ureido containing Carbonic Anhydrase inhibitors.

Akgul, O., Singh, S., Andring, J.T., McKenna, R., Selleri, S., Carta, F., Angeli, A., Supuran, C.T.

(2021) Eur J Med Chem 212: 113035-113035

PubMed: 33303238 Search on PubMed
DOI: https://doi.org/10.1016/j.ejmech.2020.113035
Primary Citation of Related Structures:
7K6I, 7K6J, 7K6K, 7K6L, 7K6T, 7K6U, 7K6X, 7K6Z

PubMed Abstract:
Here we report the synthesis of a series of taurine substituted sulfonamide derivatives 1-29 having the ureido moiety installed at the tail section as selective inhibitors of the tumor associated human (h) Carbonic Anhydrase (CA; EC 4.2.1.1) IX and XII. The series was deeply investigated for their kinetic features which demonstrated a strong dependence on the ureido moiety. High resolution X-ray crystallographic investigation on selected ligand adducts complexed with hCA II and hCA IX-mimic revealed a strong correlation between the ureido moiety and the amino acid residues Q92 and Q67 in both the hCA II and hCA IX-mimic, contributing to highly stabilized ligand-protein complex.

Organizational Affiliation

Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, 35100, Bornova, İzmir, Turkey. Electronic address: ozlem.akgul@ege.edu.tr.

Macromolecule Content

Total Structure Weight: 29.76 kDa
Atom Count: 2,235
Modelled Residue Count: 257
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VYY (Subject of Investigation/LOI) Query on VYY Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-{[(2-{[(4-methylphenyl)carbamoyl]amino}ethyl)sulfonyl]amino}benzene-1-sulfonamide C₁₆ H₂₀ N₄ O₅ S₂ YDAOBULQBPBUCA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.196
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.991	α = 90
b = 41.293	β = 103.85
c = 72.047	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-12-23

Deposition Author(s):

Andring, J.T.

Singh, S.

McKenna, R.

Revision History (Full details and data files)

Version 1.0: 2020-12-23
Type: Initial release
Version 1.1: 2021-02-24
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description