1J3I

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with WR99210, NADPH, and dUMP

Structural Biology Knowledgebase: 1J3I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1J3I

Classification: OXIDOREDUCTASE TRANSFERASE

Total Structure Weight: 146590.09

Macromolecule Entities
Molecule Chains Length Organism Details
Bifunctional dihydrofolate reductase-thymidylate synthase A, B 280 Plasmodium falciparum EC#: 1.5.1.3 IUBMB 2.1.1.45 IUBMB
Fragment: RESIDUES 1-280
Mutation: R59C, N108S
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Bifunctional dihydrofolate reductase-thymidylate synthase C, D 328 Plasmodium falciparum EC#: 1.5.1.3 IUBMB 2.1.1.45 IUBMB
Fragment: RESIDUES 281-608
Gene Name(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)
WRA
Query on WRA

A, B 6,6-DIMETHYL-1-[3-(2,4,5-TRICHLOROPHENOXY)PROPOXY]- 1,6-DIHYDRO-1,3,5-TRIAZINE-2,4-DIAMINE
4,6-DIAMINO-1,2-DIHYDRO-2,2-DIMETHYL-1-[(2,4,5- TRICHLOROPHENOXY)PROPYLOXY]-1,3,5-TRIAZINE (Synonym)
C14 H18 Cl3 N5 O2
MJZJYWCQPMNPRM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMP
Query on UMP

C, D 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP (Synonym)
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
WRA IC50: 0.57 - 18 nM (98 - 100) BindingDB
Ki: 0.011 - 0.5 nM (98 - 100) BindingDB

Ki: 0.011 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.185
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 59.12 α = 90.00
b = 157.25 β = 90.00
c = 165.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-03
  • Released Date: 2003-05-06
  • Deposition author(s): Yuvaniyama, J., Chitnumsub, P., Kamchonwongpaisan, S., Vanichtanankul, J., Sirawaraporn, W., Taylor, P., Walkinshaw, M., Yuthavong, Y.

Revision History

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