4DP3

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with P218 and NADPH

Structural Biology Knowledgebase: 4DP3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DP3

Classification: OXIDOREDUCTASE TRANSFERASE / INHIBITOR

Total Structure Weight: 146219.21

Macromolecule Entities
Molecule Chains Length Organism Details
Bifunctional dihydrofolate reductase-thymidylate synthase A, B 608 Plasmodium falciparum EC#: 1.5.1.3 IUBMB 2.1.1.45 IUBMB
Gene Name(s): DHFR-TS V1/S

Small Molecules
Ligands 3 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)
MMV
Query on MMV

A, B 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)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MMV N/A in BindingDB
Ki: 0.54 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.205
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.50 α = 90.00
b = 156.20 β = 90.00
c = 164.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-13
  • Released Date: 2012-11-14
  • Deposition author(s): Yuthavong, Y., Vilaivan, T., Kamchonwongpaisan, S., Charman, S.A., McLennan, D.N., White, K.L., Vivas, L., Bongard, E., Chitnumsub, P., Tarnchompoo, B., Thongphanchang, C., Taweechai, S., Vanichtanakul, J., Arwon, U., Fantauzzi, P., Yuvaniyama, J., Charman, W.N., Matthews, D.

Revision History

No revisions since initial release