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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

5fi8

2.320 Å

X-ray

2015-12-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dihydroorotate dehydrogenase (quinone), mitochondrial
ID:PYRD_PLAF7
AC:Q08210
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:36329
EC Number:1.3.5.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:34.835
Number of residues:21
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: FMN
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.201381.375

% Hydrophobic% Polar
33.6366.37
According to VolSite

Ligand :
5fi8_1 Structure
HET Code: ORO
Formula: C5H3N2O4
Molecular weight: 155.088 g/mol
DrugBank ID: DB02262
Buried Surface Area:76.43 %
Polar Surface area: 98.33 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-47.960993.1505-7.07618


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
N1OD1ASN- 2742.95170.79H-Bond
(Ligand Donor)
O2ND2ASN- 2743.05169.11H-Bond
(Protein Donor)
O71NGLY- 2772.89146.44H-Bond
(Protein Donor)
O72NPHE- 2783.01138.74H-Bond
(Protein Donor)
O4ND2ASN- 3423159.45H-Bond
(Protein Donor)
N3OD1ASN- 4582.78176.82H-Bond
(Ligand Donor)
O4ND2ASN- 4582.89162.62H-Bond
(Protein Donor)
O2OG1THR- 4592.8163.74H-Bond
(Protein Donor)