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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:

3gz3

1.900 Å

X-ray

2009-04-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dihydroorotate dehydrogenase (fumarate)
ID:Q4QEW7_LEIMA
AC:Q4QEW7
Organism:Leishmania major
Reign:Eukaryota
TaxID:5664
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.828
Number of residues:22
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: FMN
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.140421.875

% Hydrophobic% Polar
24.0076.00
According to VolSite

Ligand :
3gz3_1 Structure
HET Code: ORO
Formula: C5H3N2O4
Molecular weight: 155.088 g/mol
DrugBank ID: DB02262
Buried Surface Area:71.37 %
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
52.7125-21.7677-15.1985


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
O71NZLYS- 442.96154.21H-Bond
(Protein Donor)
O71NZLYS- 442.960Ionic
(Protein Cationic)
N1OD1ASN- 682.95170.46H-Bond
(Ligand Donor)
O2ND2ASN- 682.97163.78H-Bond
(Protein Donor)
O72NGLY- 712.83142.55H-Bond
(Protein Donor)
O71NLEU- 722.92139.26H-Bond
(Protein Donor)
O4ND2ASN- 1283.01173.76H-Bond
(Protein Donor)
N3OD1ASN- 1952.67173.7H-Bond
(Ligand Donor)
O4ND2ASN- 1952.85158.1H-Bond
(Protein Donor)
O2OGSER- 1962.52135.26H-Bond
(Protein Donor)