6SWM | pdb_00006swm

selenol bound carbonic anhydrase I

• PDB DOI: https://doi.org/10.2210/pdb6SWM/pdb

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


• Deposited: 2019-09-22 Released: 2020-10-07 
• Deposition Author(s): Angeli, A., Ferraroni, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.330 (Depositor), 0.338 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.282 (DCC) 
• R-Value Observed: 
  0.275 (Depositor) 

Starting Model: experimental

Literature

Selenols: a new class of carbonic anhydrase inhibitors.

Angeli, A., Tanini, D., Nocentini, A., Capperucci, A., Ferraroni, M., Gratteri, P., Supuran, C.T.

(2019) Chem Commun (Camb) 55: 648-651

• PubMed: 30560259 
• DOI: https://doi.org/10.1039/c8cc08562e
• Primary Citation Related Structures: 
  6HWZ, 6HX5, 6SWM


• PubMed Abstract: 
  

  Stable aryl selenols were obtained through a convenient procedure. Selenols represent a new chemotype acting as carbonic anhydrase inhibitors (CAIs), inhibiting four human isoforms, CAs I, II, VII and the tumor-associated CA IX. X-ray crystallographic, physical and computational studies provided insights into the binding mode of this conceptually new class of CAIs.

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Organizational Affiliation: 
• University of Florence, NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy. [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: 58.33 kDa 
• Atom Count: 4,103 
• Modeled Residue Count: 512 
• 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 GTEx:  ENSG00000133742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LVW (Subject of Investigation/LOI)	D [auth A], F [auth B]	(2~{R})-1-prop-2-enoxy-3-selanyl-propan-2-ol C6 H12 O2 Se YQCUFGFATQCBJJ-ZCFIWIBFSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.330 (Depositor), 0.338 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.282 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.789	α = 90
b = 69.586	β = 90
c = 119.191	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: 2020-10-07 
Deposition Author(s): Angeli, A., Ferraroni, M.

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2021-04-21
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2025-10-01
  Changes: Derived calculations, Structure summary