5AMD | pdb_00005amd

Three dimensional structure of human carbonic anhydrase II in complex with 2-((2-Phenylethyl)sulfamoyl)-4-sulfamoylbenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb5AMD/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-10 Released: 2015-04-08 
• Deposition Author(s): Leitans, J., Tars, K., Zalubovskis, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

X-Ray Crystallography-Promoted Drug Design of Carbonic Anhydrase Inhibitors.

Ivanova, J., Leitans, J., Tanc, M., Kazaks, A., Zalubovskis, R., Supuran, C.T., Tars, K.

(2015) Chem Commun (Camb) 51: 7108

• PubMed: 25813715 
• DOI: https://doi.org/10.1039/c5cc01854d
• Primary Citation of Related Structures:  
  5AMD, 5AMG, 5AML


• PubMed Abstract: 
  

  1-N-Alkylated-6-sulfamoyl saccharin derivatives were prepared and assayed as carbonic anhydrase inhibitors (CAIs). During X-ray crystallographic experiments an unexpected hydrolysis of the isothiazole ring was evidenced which allowed us to prepare highly potent enzyme inhibitors with selectivity for some isoforms with medical applications.

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Organizational Affiliation: 
• Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia. [e-mail].

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: 29.61 kDa 
• Atom Count: 2,493 
• Modeled Residue Count: 257 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE 2	A	259	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
45I	C [auth A]	2-[(2-PHENYLETHYL)SULFAMOYL]-4-SULFAMOYLBENZOIC ACID C15 H16 N2 O6 S2 UPBRYTJLOYELEW-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.16	α = 90
b = 41.53	β = 104.47
c = 72.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Leitans, J., Tars, K., Zalubovskis, R.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description