3I65

Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.212

Literature

Macromolecules
Sequence Display for 3I65

Classification: OXIDOREDUCTASE

Total Structure Weight: 47771.51

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydroorotate dehydrogenase homolog, mitochondrial A 415 Plasmodium falciparum EC#: 1.3.5.2 IUBMB
Fragment: UNP residues 158-569 with 384-413 deleted
Mutation: ΔS384, ΔT385, ΔY386, ΔN387, ΔE388, ΔD389, ΔN390, ΔK391, ΔI392, ΔV393, ΔE394, ΔK395, ΔK396, ΔN397, ΔN398, ΔF399, ΔN400, ΔK401, ΔN402, ΔN403, ΔS404, ΔH405, ΔM406, ΔM407, ΔK408, ΔD409, ΔA410, ΔK411, ΔD412, ΔN413
Gene Name(s): PFF0160c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Dihydroorotate Dehydrogenases (DHODH, class 2)

Protein Name: Dihydroorotate Dehydrogenase with triazolopyrimidine-based inhibitor DSM1


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FMN
Query on FMN

A FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
JZ8
Query on JZ8

A 5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5- a]pyrimidine-3,8-diium
C16 H15 N5
GNJXIZOPHGMAQW-UHFFFAOYSA-P
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LDA
Query on LDA

A LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ORO
Query on ORO

A OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
JZ8 N/A in BindingDB
IC50: 47 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.212
  • Space Group: P 64

Unit Cell:

Length (Å) Angle (°)
a = 85.86 α = 90.00
b = 85.86 β = 90.00
c = 138.35 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-06
  • Released Date: 2009-07-28
  • Deposition author(s): Deng, X., Phillips, M.A.

Revision History

  • 2011-07-13
    Type: Version format compliance