1YDD

STRUCTURAL BASIS OF INHIBITOR AFFINITY TO VARIANTS OF HUMAN CARBONIC ANHYDRASE II

Structural Biology Knowledgebase: 1YDD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Observed: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YDD

Classification: HYDRO-LYASE

Total Structure Weight: 29690.31

Macromolecule Entities
Molecule Chains Length Organism Details
CARBONIC ANHYDRASE II A 259 Homo sapiens EC#: 4.2.1.1 IUBMB
Mutation: L198R
Gene Name(s): CA2 Gene View

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

A 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE
C4 H6 N4 O3 S2
BZKPWHYZMXOIDC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HG
Query on HG

A MERCURY (II) ION
Hg
BQPIGGFYSBELGY-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 %)
AZM IC50: 3.4 - 8300 nM (99) BindingDB
Kd: 6.8 - 38 nM (99) BindingDB
Ki: 3.3 - 12000 nM (98 - 99) BindingDB

Kd: 86 nM  BindingMOAD
Kd: 86 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Observed: 0.187
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 42.70 α = 90.00
b = 41.70 β = 104.60
c = 73.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1994-12-22
  • Released Date: 1995-02-14
  • Deposition author(s): Nair, S.K., Christianson, D.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4