1PD8

Analysis of Three Crystal Structure Determinations of a 5-Methyl-6-N-Methylanilino Pyridopyrimidine Antifolate Complex with Human Dihydrofolate Reductase

Structural Biology Knowledgebase: 1PD8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 1PD8

Classification: OXIDOREDUCTASE

Total Structure Weight: 22479.56

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydrofolate reductase A 186 Homo sapiens EC#: 1.5.1.3 IUBMB
Gene Name(s): DHFR Gene View
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 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO4
Query on CO4

A 2,4-DIAMINO-5-METHYL-6-[(3,4,5-TRIMETHOXY- N-METHYLANILINO)METHYL]PYRIDO[2,3-D]PYRIMIDINE
C19 H24 N6 O3
PEGMMEYCSOZKIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CO4 IC50: 7.6 nM (89) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.173
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 85.87 α = 90.00
b = 85.87 β = 90.00
c = 77.64 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-19
  • Released Date: 2003-12-09
  • Deposition author(s): Cody, V., Luft, J.R., Pangborn, W., Gangjee, A.

Revision History

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