4DDR

Human dihydrofolate reductase complexed with NADPH and P218

Structural Biology Knowledgebase: 4DDR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DDR

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR

Total Structure Weight: 22455.54

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

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MMV
Query on MMV

A 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5- yl)oxy]propoxy}phenyl)propanoic acid
C18 H24 N4 O4
VDGXZSSDCDPCRF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MMV N/A in BindingDB
Ki: 2841 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.205
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 85.29 α = 90.00
b = 85.29 β = 90.00
c = 77.13 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-19
  • Released Date: 2012-11-14
  • Deposition author(s): Yuthavong, Y., Tarnchompoo, B., Vilaivan, T., Chitnumsub, P., Kamchonwongpaisan, S., Charman, S.A., McLennan, D.N., White, K.L., Vivas, L., Bongard, E., Thongphanchang, C., Taweechai, S., Vanichtanankul, J., Rattanajak, R., Arwon, U., Fantauzzi, P., Yuvaniyama, J., Charman, W.N., Matthews, D.

Revision History

No revisions since initial release