4MDG

Closo Carborane Carbonic Anhydrase Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • 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.


  • 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).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2258Homo sapiensMutation(s): 0 
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
25X
Query on 25X

Download Ideal Coordinates CCD File 
C [auth A]1-(sulfamoylamino)methyl-1,2-dicarba-closo-dodecaborane
C3 H5 B10 N2 O2 S
WQWJNYUSODCUQX-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
25X Binding MOAD:  4MDG Ki: 700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.1α = 90
b = 41.57β = 104.13
c = 72.13γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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