4MDM | pdb_00004mdm

Nido-Carborane Carbonic Anhydrase Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4MDM/pdb

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


• Deposited: 2013-08-23 Released: 2014-01-01 
• Deposition Author(s): Brynda, J., Mader, P., Rezacova, P., Cigler, P., Gruner, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Carborane-based carbonic anhydrase inhibitors.

Brynda, J., Mader, P., Sicha, V., Fabry, M., Poncova, K., Bakardiev, M., Gruner, B., Cigler, P., Rezacova, P.

(2013) Angew Chem Int Ed Engl 52: 13760-13763

• PubMed: 24307504 
• DOI: https://doi.org/10.1002/anie.201307583
• Primary Citation of Related Structures:  
  4MDG, 4MDL, 4MDM


• PubMed Abstract: 
  

  CA inhibitors: Human carbonic anhydrases (CAs) are diagnostic and therapeutic targets. Various carborane cages are shown to act as active-site-directed inhibitors, and substitution with a sulfamide group and other substituents leads to compounds with high selectivity towards the cancer-specific isozyme IX. Crystal structures of the carboranes in the active site provide information that can be applied to the structure-based design of specific inhibitors.

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Organizational Affiliation: 

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i. Vídeňská 1083, 142 20 Prague 4 (Czech Republic); Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, 16610 Prague 6 (Czech Republic).

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: 29.37 kDa 
• Atom Count: 2,310 
• Modelled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	258	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
26E	C [auth A]	7-(sulfamoylamino)methyl-7,8-dicarba-nido-undecaborane C3 H5 B9 N2 O2 S VRKHBQSBPLXCRB-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.01	α = 90
b = 41.3	β = 104.17
c = 72.06	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-01 
Deposition Author(s): Brynda, J., Mader, P., Rezacova, P., Cigler, P., Gruner, B.

Revision History  

• Version 1.0: 2014-01-01
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations