6I0L

Crystal structure of human carbonic anhydrase I in complex with the 1-[4-chloro-3-(trifluoromethyl)phenyl]-3-[2-(4-sulfamoylphenyl)ethyl]urea inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb6I0L/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2018-10-26 Released: 2019-11-20 
• Deposition Author(s): Ferraroni, M., Supuran, C.T., Bozdag, M., Chiapponi, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Carbonic anhydrase inhibitors based on sorafenib scaffold: Design, synthesis, crystallographic investigation and effects on primary breast cancer cells.

Bozdag, M., Ferraroni, M., Ward, C., Carta, F., Bua, S., Angeli, A., Langdon, S.P., Kunkler, I.H., Al-Tamimi, A.S., Supuran, C.T.

(2019) Eur J Med Chem 182: 111600-111600

• PubMed: 31419777 
• DOI: https://doi.org/10.1016/j.ejmech.2019.111600
• Primary Citation of Related Structures:  
  6I0J, 6I0L


• PubMed Abstract: 
  

Carbonic anhydrase inhibitors (CAIs) of the sulfonamide, sulfamate and coumarin classes bearing the phenylureido tail found in the clinically used drug Sorafenib, a multikinase inhibitor actually used for the management of hepatocellular carcinomas, are reported. All compounds were assayed on human (h) CA isoforms I, II, VII and IX, involved in various pathologies. Among the sulfonamides, several compounds were selective for inhibiting hCA IX, with K _I values in the low nanomolar ranges (i.e. 0.7-30.2 nM). We explored the binding modes of such compounds by means of X-ray crystallographic studies on isoform hCA I in adduct with one sulfonamide and a sulfamate inhibitor. Antiproliferative properties of some sulfamates on breast tumor cell lines were also investigated.

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Organizational Affiliation: 

University of Florence, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.12 kDa 
• Atom Count: 4,618 
• Modelled Residue Count: 514 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 1	A, B	261	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GZH (Subject of Investigation/LOI)	D [auth A], H [auth B]	1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[2-(4-sulfamoylphenyl)ethyl]urea C16 H15 Cl F3 N3 O3 S FBVAPDWPSNARKD-UHFFFAOYSA-N
GOL	E [auth A], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
ACT	BindingDB:  6I0L	Ki: 1.08e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.461	α = 90
b = 70.453	β = 90
c = 121.56	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Ferraroni, M., Supuran, C.T., Bozdag, M., Chiapponi, D.

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references, Derived calculations