9GOO | pdb_00009goo

Crystal structure of human carbonic anhydrase II in complex with PCI-27483

• PDB DOI: https://doi.org/10.2210/pdb9GOO/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-05 Released: 2025-09-17 
• Deposition Author(s): Angeli, A., Ferraroni, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.163 (DCC) 

Starting Model: experimental

Literature

Exploring the Polypharmacological Potential of PCI-27483: A Selective Inhibitor of Carbonic Anhydrases IX and XII.

D'Agostino, I., Bonardi, A., Ferraroni, M., Gratteri, P., Angeli, A., Supuran, C.T.

(2024) ACS Med Chem Lett 15: 2042-2045

• PubMed: 39563799 
• DOI: https://doi.org/10.1021/acsmedchemlett.4c00443
• Primary Citation Related Structures: 
  9GOO


• PubMed Abstract: 
  

  PCI-27483, originally developed as a potent and selective inhibitor of the serine protease Factor VIIa (FVIIa) in complex with tissue factor (TF), has demonstrated significant promise in cancer therapy. In addition to its primary mechanism of action, the presence of a sulfonamide moiety in the PCI-27483 structure suggests further activities through the inhibition of carbonic anhydrases (CAs), particularly the tumor-associated human (h)CA isoforms hCA IX and XII. This study investigates the inhibitory activity of PCI-27483 against the complete panel of active hCAs, highlighting its polypharmacological potential in cancer treatment. X-ray crystallography and molecular docking studies elucidated the structural features underlying its selective inhibitory activity toward hCA IX and XII, offering insights into its dual-targeting pathway.

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Organizational Affiliation: 
• Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Florence, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.01 kDa 
• Atom Count: 2,410 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A [auth AAA]	260	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IOK (Subject of Investigation/LOI)	B [auth AAA]	PCI-27483 C26 H24 N6 O9 S WDJHHCAKBRKCLW-IBGZPJMESA-N
ZN	D [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.163 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.509	α = 90
b = 41.737	β = 104.628
c = 72.501	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Angeli, A., Ferraroni, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release
  
• Version 1.1: 2025-12-03
  Changes: Derived calculations, Structure summary
• Version 1.2: 2026-04-01
  Changes: Database references