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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:

3dg8

2.580 Å

X-ray

2008-06-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Bifunctional dihydrofolate reductase-thymidylate synthase
ID:DRTS_PLAFK
AC:P13922
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:5839
EC Number:1.5.1.3


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:71.221
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NDP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.048654.750

% Hydrophobic% Polar
56.1943.81
According to VolSite

Ligand :
3dg8_2 Structure
HET Code: RJ6
Formula: C10H17N5O2
Molecular weight: 239.274 g/mol
DrugBank ID: DB08479
Buried Surface Area:67.88 %
Polar Surface area: 119.72 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 5
Rings: 1
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
30.2205-30.20176.76888


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
C4CD2LEU- 464.410Hydrophobic
C10CGLEU- 463.320Hydrophobic
N17OD2ASP- 543.17123.36H-Bond
(Ligand Donor)
N17OD1ASP- 543.1143.36H-Bond
(Ligand Donor)
C8CZPHE- 584.280Hydrophobic
C8SDMET- 1043.780Hydrophobic
C1CD1ILE- 1124.360Hydrophobic
C2CG1ILE- 1124.110Hydrophobic
C8CD1ILE- 1123.660Hydrophobic
C8CD1LEU- 1193.480Hydrophobic
C8CD1LEU- 1643.360Hydrophobic
C10C2DNDP- 6103.960Hydrophobic