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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:

2w9s

1.800 Å

X-ray

2009-01-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dihydrofolate reductase type 1 from Tn4003
ID:DYRA_STAAU
AC:P13955
Organism:Staphylococcus aureus
Reign:Bacteria
TaxID:1280
EC Number:1.5.1.3


Chains:

Chain Name:Percentage of Residues
within binding site
B4 %
E96 %


Ligand binding site composition:

B-Factor:31.081
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.4142136.375

% Hydrophobic% Polar
47.3952.61
According to VolSite

Ligand :
2w9s_5 Structure
HET Code: TOP
Formula: C14H18N4O3
Molecular weight: 290.318 g/mol
DrugBank ID: DB00440
Buried Surface Area:57.66 %
Polar Surface area: 105.51 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-12.958822.839311.7635


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
N7OILE- 52.74157.44H-Bond
(Ligand Donor)
C14CD2LEU- 203.850Hydrophobic
C15CD1LEU- 204.260Hydrophobic
C12CGLEU- 203.850Hydrophobic
N2OD2ASP- 272.73167.03H-Bond
(Ligand Donor)
N4OD2ASP- 273.3131.28H-Bond
(Ligand Donor)
N4OD1ASP- 272.66168.99H-Bond
(Ligand Donor)
C20CD2LEU- 284.020Hydrophobic
C8CD1ILE- 314.160Hydrophobic
C20CD1ILE- 314.310Hydrophobic
C21CD1ILE- 314.360Hydrophobic
C17CBSER- 494.310Hydrophobic
C17CG1ILE- 504.30Hydrophobic
C20CD1ILE- 504.450Hydrophobic
C21CD1ILE- 504.290Hydrophobic
C15CG1ILE- 504.040Hydrophobic
N7OPHE- 922.94146.36H-Bond
(Ligand Donor)
C9CZPHE- 923.840Hydrophobic
C20CZPHE- 924.440Hydrophobic