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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:

3gdu

3.000 Å

X-ray

2009-02-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Serine endoprotease DegS
ID:DEGS_ECOLI
AC:P0AEE3
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:3.4.21.107


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:99.999
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.953604.125

% Hydrophobic% Polar
44.1355.87
According to VolSite

Ligand :
3gdu_3 Structure
HET Code: TYR_ARG_PHE
Formula: C24H33N6O5
Molecular weight: 485.556 g/mol
DrugBank ID: -
Buried Surface Area:44.25 %
Polar Surface area: 212.2 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 7
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 2
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
-15.417774.18975.95189


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
ONH1ARG- 1863.48143.9H-Bond
(Protein Donor)
CZCD1ILE- 2593.980Hydrophobic
CD2CD1ILE- 2593.430Hydrophobic
OXTNILE- 2592.99162.5H-Bond
(Protein Donor)
NOILE- 2613.02166.88H-Bond
(Ligand Donor)
ONILE- 2612.87170.54H-Bond
(Protein Donor)
NOGLY- 2633.48139.25H-Bond
(Ligand Donor)
ONGLY- 2633.2148.11H-Bond
(Protein Donor)
CE1CD1LEU- 3164.320Hydrophobic
CE2CG2THR- 3184.090Hydrophobic
CD1SDMET- 3193.860Hydrophobic
CE1CEMET- 3194.20Hydrophobic
CBCBMET- 3193.490Hydrophobic
CD2CG2VAL- 3223.950Hydrophobic