3PO6

Crystal structure of human carbonic anhydrase II with 6,7-Dimethoxy-1-methyl-3,4-dihydroisoquinoline-2(1H)-sulfonamide

• PDB DOI: https://doi.org/10.2210/pdb3PO6/pdb

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


• Deposited: 2010-11-22 Released: 2011-04-06 
• Deposition Author(s): Mader, P., Brynda, J., Gitto, R., Agnello, S., Ferro, S., De Luca, L., Vullo, D., Supuran, C.T., Chimirri, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.175 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

Literature

Structural basis for the interaction between carbonic anhydrase and 1,2,3,4-tetrahydroisoquinolin-2-ylsulfonamides.

Mader, P., Brynda, J., Gitto, R., Agnello, S., Pachl, P., Supuran, C.T., Chimirri, A., Rezacova, P.

(2011) J Med Chem 54: 2522-2526

• PubMed: 21395315 
• DOI: https://doi.org/10.1021/jm2000213
• Primary Citation of Related Structures:  
  3PO6


• PubMed Abstract: 
  

  Isoquinolinesulfonamides inhibit human carbonic anhydrases (hCAs) and display selectivity toward therapeutically relevant isozymes. The crystal structure of hCA II in complex with 6,7-dimethoxy-1-methyl-1,2,3,4-tetrahydroisoquinolin-2-ylsulfonamide revealed unusual inhibitor binding. Structural analyses allowed for discerning the fine details of the inhibitor binding mode to the active site, thus providing clues for the future design of even more selective inhibitors for druggable isoforms such as the cancer associated hCA IX and neuronal hCA VII.

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Organizational Affiliation: 

Department of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, 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: 30.22 kDa 
• Atom Count: 2,510 
• Modelled Residue Count: 258 
• 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
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RDT	D [auth A]	(1R)-6,7-dimethoxy-1-methyl-3,4-dihydroisoquinoline-2(1H)-sulfonamide C12 H18 N2 O4 S GUJQIHRSATWPQA-MRVPVSSYSA-N
DT9	C [auth A]	(1S)-6,7-dimethoxy-1-methyl-3,4-dihydroisoquinoline-2(1H)-sulfonamide C12 H18 N2 O4 S GUJQIHRSATWPQA-QMMMGPOBSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
DT9	PDBBind:  3PO6	Ki: 87.3 (nM) from 1 assay(s)
ACT	BindingDB:  3PO6	Ki: 1.30e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.175 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.18	α = 90
b = 41.21	β = 104.31
c = 72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Mader, P., Brynda, J., Gitto, R., Agnello, S., Ferro, S., De Luca, L., Vullo, D., Supuran, C.T., Chimirri, A.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-07
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations