3EEM

Candida glabrata Dihydrofolate Reductase complexed with 2,4-diamino-5-[3-methyl-3-(3-methoxy-5-(2,6-dimethylphenyl)phenyl)prop-1-ynyl]-6-methylpyrimidine(UCP111D26M) and NADPH

Structural Biology Knowledgebase: 3EEM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EEM

Classification: OXIDOREDUCTASE

Total Structure Weight: 55118.92

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydrofolate reductase A, B 227 Candida glabrata Gene Name(s): CAGL0J03894g
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
53V
Query on 53V

A, B 5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl- 3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4- diamine
C24 H26 N4 O
XZXVRKHUCSXVBM-AWEZNQCLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
53V IC50: 5.5 nM (100) BindingDB

IC50: 5.5 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.169
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.82 α = 90.00
b = 42.82 β = 90.00
c = 231.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-04
  • Released Date: 2009-08-18
  • Deposition author(s): Liu, J., Anderson, A.

Revision History

  • 2013-11-20
    Type: Non-polymer description | Details: Corrected ligand label
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4