scPDB - 3i0o entry

Protein Data Bank Entry:

PDB ID : 3i0o

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2009-06-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

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

Ligandability	Volume (Å3)
0.361	756.000

% Hydrophobic	% Polar
33.48	66.52
According to VolSite

Ligand :

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

X	Y	Z
36.527	-8.24842	16.8352

Binding mode :

What is Poseview ?

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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C2	CZ	PHE- 109	4.21	0	Hydrophobic	false
C2M	CE1	PHE- 109	3.99	0	Hydrophobic	false
N10	OD2	ASP- 212	3.66	0	Ionic (Ligand Cationic)	false
O11	OD1	ASP- 212	3.37	126.95	H-Bond (Ligand Donor)	false
O11	NE2	HIS- 214	3.34	177.4	H-Bond (Protein Donor)	false
C6	CG1	VAL- 250	4.11	0	Hydrophobic	false
O5	NH2	ARG- 284	3.05	131.11	H-Bond (Protein Donor)	false
O5	NH1	ARG- 284	3.07	130.6	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 284	3	135.07	H-Bond (Protein Donor)	false
O5	OD2	ASP- 288	2.69	150	H-Bond (Ligand Donor)	false
N8	OD1	ASP- 288	2.79	149	H-Bond (Ligand Donor)	false
N8	OD1	ASP- 288	2.79	0	Ionic (Ligand Cationic)	false
N8	OH	TYR- 292	3.07	168.7	H-Bond (Ligand Donor)	false
O4A	OH	TYR- 292	3.23	161.17	H-Bond (Ligand Donor)	false
C2M	CZ	TYR- 312	3.69	0	Hydrophobic	false
C3	CG	TYR- 312	3.92	0	Hydrophobic	false