3S8X

Crystal structure of human carbonic anhydrase isozyme II with 4-{[(4-methyl-6-oxo-1,6-dihydro-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide

Structural Biology Knowledgebase: 3S8X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.142

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3S8X

Classification: lyase / lyase inhibitor

Total Structure Weight: 30013.49

Macromolecule Entities
Molecule Chains Length Organism Details
Carbonic anhydrase 2 A 260 Homo sapiens EC#: 4.2.1.1 IUBMB
Gene Name(s): CA2 Gene View

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
E59
Query on E59

A 4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin- 2-yl)sulfanyl]acetyl}benzenesulfonamide
C13 H13 N3 O4 S2
UZGWPPSMIYIVBV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCN
Query on BCN

A BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
E59 N/A in BindingDB
Kd: 70 nM  BindingMOAD
Kd: 50 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.142
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.21 α = 90.00
b = 41.18 β = 104.29
c = 71.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-31
  • Released Date: 2012-04-11
  • Deposition author(s): Grazulis, S., Manakova, E., Tamulaitiene, G.

Revision History

  • 2012-05-16
    Type: Citation | Details: Citation update