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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:

3q2m

2.900 Å

X-ray

2010-12-20

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:56.388
Number of residues:19
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.091543.375

% Hydrophobic% Polar
63.3536.65
According to VolSite

Ligand :
3q2m_1 Structure
HET Code: CKI
Formula: C11H13ClN3O2S
Molecular weight: 286.758 g/mol
DrugBank ID: DB03693
Buried Surface Area:52.79 %
Polar Surface area: 95.07 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-0.72883326.501134.6647


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
C4CBPHE- 504.040Hydrophobic
CL5CE1PHE- 504.050Hydrophobic
DuArDuArPHE- 503.810Aromatic Face/Face
C4CD1ILE- 783.610Hydrophobic
N2NILE- 1032.8144.77H-Bond
(Protein Donor)
N2'OALA- 1053.42121.27H-Bond
(Ligand Donor)
C9CD1LEU- 2194.50Hydrophobic
CL5CBILE- 2293.980Hydrophobic
C6CD1ILE- 2293.760Hydrophobic