6YRI | pdb_00006yri

THE CRYSTAL STRUCTURE OF THE COMPLEX OF HCAII WITH CAFFEIC ACID

• PDB DOI: https://doi.org/10.2210/pdb6YRI/pdb

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


• Deposited: 2020-04-20 Released: 2021-03-31 
• Deposition Author(s): D'Ambrosio, K., De Simone, G.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.193 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.167 (DCC) 

Starting Model: experimental

Literature

Catechols: a new class of carbonic anhydrase inhibitors.

D'Ambrosio, K., Carradori, S., Cesa, S., Angeli, A., Monti, S.M., Supuran, C.T., De Simone, G.

(2020) Chem Commun (Camb) 56: 13033-13036

• PubMed: 33000794 
• DOI: https://doi.org/10.1039/d0cc05172a
• Primary Citation Related Structures: 
  6YRI


• PubMed Abstract: 
  

  To date, catechols have been only poorly investigated as carbonic anhydrase (CA) inhibitors. Here we report the first structural information on the CA inhibition mechanism of these molecules, showing that they adopt a peculiar binding mode to the enzyme active site which involves the zinc-bound water molecule and the "deep water".

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Organizational Affiliation: 
• Istituto di Biostrutture e Bioimmagini-CNR, Naples, Italy. [e-mail] [e-mail].
Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy.
Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, 00185 Rome, Italy.
Neurofarba Department, Università degli Studi di Firenze, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.91 kDa 
• Atom Count: 2,411 
• Modeled Residue Count: 257 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	262	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
DHC (Subject of Investigation/LOI)	C [auth A]	CAFFEIC ACID C9 H8 O4 QAIPRVGONGVQAS-DUXPYHPUSA-N
GOL (Subject of Investigation/LOI)	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DHC	BindingDB:  6YRI	Ki: 1610 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.193 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.167 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.25	α = 90
b = 41.35	β = 104.27
c = 72.1	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
O	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): D'Ambrosio, K., De Simone, G.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	MOLIM ONCOBRAIN LAB

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description