3F7U

Crystal Structure of soluble domain of CA4 in complex with small molecule.

• PDB DOI: https://doi.org/10.2210/pdb3F7U/pdb

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


• Deposited: 2008-11-10 Released: 2009-09-22 
• Deposition Author(s): Pauly, T.A., Ferre, R.A.A., Greasley, S.E., Paz, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Thioether benzenesulfonamide inhibitors of carbonic anhydrases II and IV: structure-based drug design, synthesis, and biological evaluation.

Vernier, W., Chong, W., Rewolinski, D., Greasley, S., Pauly, T., Shaw, M., Dinh, D., Ferre, R.A., Nukui, S., Ornelas, M., Reyner, E.

(2010) Bioorg Med Chem 18: 3307-3319

• PubMed: 20363633 
• DOI: https://doi.org/10.1016/j.bmc.2010.03.014
• Primary Citation of Related Structures:  
  3F7B, 3F7U, 3FW3


• PubMed Abstract: 
  

  A novel series of potent thioether benzenesulfonamide inhibitors of carbonic anhydrases II and IV was discovered using structure-based drug design. Synthesis, structure-activity relationship, and optimization of physicochemical properties are described. Low nanomolar potency was achieved, and selected compounds with improved thermodynamic solubility showed promising in vitro inhibition of carbonic anhydrase activity in rabbit iris ciliary body homogenate.

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Organizational Affiliation: 

Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Drive, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 123.25 kDa 
• Atom Count: 8,351 
• Modelled Residue Count: 988 
• Deposited Residue Count: 1,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 4	A, B, C, D	266	Homo sapiens	Mutation(s): 0  Gene Names: CA4 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P22748 (Homo sapiens) Go to UniProtKB:  P22748
PHAROS:  P22748 GTEx:  ENSG00000167434

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG4	F [auth A], H [auth B], J [auth C], L [auth D]	N-(3-methoxypropyl)-2-(phenylsulfanyl)-5-sulfamoylpyridine-3-carboxamide C16 H19 N3 O4 S2 YFGZGDDAWQULRR-UHFFFAOYSA-N
ZN	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AG4	PDBBind:  3F7U	IC50: 246 (nM) from 1 assay(s)
	BindingDB:  3F7U	IC50: 246 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.886	α = 90
b = 123.83	β = 90
c = 152.723	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Pauly, T.A., Ferre, R.A.A., Greasley, S.E., Paz, R.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description