4WL4 | pdb_00004wl4

Crystal structure of human carbonic anhydrase II in complex with the 6-hydroxy-chromene-2-thione inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4WL4/pdb

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


• Deposited: 2014-10-06 Released: 2015-10-14 
• Deposition Author(s): Ferraroni, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.130 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.109 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.110 (Depositor) 

Starting Model: experimental

Literature

New classes of carbonic anhydrase inhibitors

Ferraroni, M., Supuran, C.T., Carta, F., Bozdag, M., Scozzafava, A.

To be published.

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: 29.59 kDa 
• Atom Count: 2,552 
• Modeled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  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
FC5	C [auth A]	6-hydroxy-2H-chromene-2-thione C9 H6 O2 S FGHZVFOCIYABBE-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FC5	BindingDB:  4WL4	Ki: min: 2.00e+5, max: 2.85e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.130 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.109 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.110 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.264	α = 90
b = 41.367	β = 104.21
c = 72.276	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Ferraroni, M.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description