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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:

3i0o

2.400 Å

X-ray

2009-06-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Spectinomycin phosphotransferase
ID:O06916_LEGPN
AC:O06916
Organism:Legionella pneumophila
Reign:Bacteria
TaxID:446
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:44.996
Number of residues:23
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors: ADP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.361756.000

% Hydrophobic% Polar
33.4866.52
According to VolSite

Ligand :
3i0o_1 Structure
HET Code: SMI
Formula: C14H28N2O8
Molecular weight: 352.381 g/mol
DrugBank ID: -
Buried Surface Area:43.55 %
Polar Surface area: 162.06 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 7
Rings: 3
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 2
Rule of Five Violation: 1
Rotatable Bonds: 2

Mass center Coordinates

XYZ
36.527-8.2484216.8352


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
C2CZPHE- 1094.210Hydrophobic
C2MCE1PHE- 1093.990Hydrophobic
N10OD2ASP- 2123.660Ionic
(Ligand Cationic)
O11OD1ASP- 2123.37126.95H-Bond
(Ligand Donor)
O11NE2HIS- 2143.34177.4H-Bond
(Protein Donor)
C6CG1VAL- 2504.110Hydrophobic
O5NH2ARG- 2843.05131.11H-Bond
(Protein Donor)
O5NH1ARG- 2843.07130.6H-Bond
(Protein Donor)
O2BNH2ARG- 2843135.07H-Bond
(Protein Donor)
O5OD2ASP- 2882.69150H-Bond
(Ligand Donor)
N8OD1ASP- 2882.79149H-Bond
(Ligand Donor)
N8OD1ASP- 2882.790Ionic
(Ligand Cationic)
N8OHTYR- 2923.07168.7H-Bond
(Ligand Donor)
O4AOHTYR- 2923.23161.17H-Bond
(Ligand Donor)
C2MCZTYR- 3123.690Hydrophobic
C3CGTYR- 3123.920Hydrophobic