3NXO

Perferential Selection of Isomer Binding from Chiral Mixtures: Alternate Binding Modes Observed for the E- and Z-isomers of a Series of 5-Substituted 2,4-Diaminofuro[2,3-d]pyrimidines as Ternary Complexes with NADPH and Human Dihydrofolate Reductase

Structural Biology Knowledgebase: 3NXO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 3NXO

Classification: OXIDOREDUCTASE

Total Structure Weight: 22927.81

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydrofolate reductase A 186 Homo sapiens EC#: 1.5.1.3 IUBMB
Mutation: K63R
Gene Name(s): DHFR Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D2B
Query on D2B

A 5-[(1Z)-2-(2-methoxyphenyl)-3-methylbut-1- en-1-yl]furo[2,3-d]pyrimidine-2,4-diamine
C18 H20 N4 O2
ZBHMLBFDTQKTKI-JYRVWZFOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
D2B IC50: 4140 - 11900 nM (89 - 99) BindingDB

Ki: 830 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.191
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 84.15 α = 90.00
b = 84.15 β = 90.00
c = 77.97 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-07-14
  • Released Date: 2010-12-01
  • Deposition author(s): Cody, V.

Revision History

  • 2012-03-21
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4