scPDB - 1bo4 entry

Protein Data Bank Entry:

PDB ID : 1bo4

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1998-08-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminoglycoside-(3)-N-acetyltransferase
ID:	Q53396_SERMA
AC:	Q53396
Organism:	Serratia marcescens
Reign:	Bacteria
TaxID:	615
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	28.319
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.317	718.875

% Hydrophobic	% Polar
28.64	71.36
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	40.04 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
17.7919	45.7575	28.2936

Binding mode :

What is Poseview ?

2D View
3D View

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
C6P	CE1	PHE- 51	3.59	0	Hydrophobic	false
CDP	CD2	LEU- 111	3.6	0	Hydrophobic	false
C2P	CB	LEU- 111	3.94	0	Hydrophobic	false
S1P	CD1	LEU- 111	4.44	0	Hydrophobic	false
N4P	O	LEU- 111	2.89	162.54	H-Bond (Ligand Donor)	false
C6P	CB	ALA- 112	4.36	0	Hydrophobic	false
CDP	CG2	VAL- 113	4.23	0	Hydrophobic	false
CAP	CB	VAL- 113	4.42	0	Hydrophobic	false
O9P	N	VAL- 113	2.74	165.05	H-Bond (Protein Donor)	false
CAP	CD	ARG- 118	3.81	0	Hydrophobic	false
O8A	NH1	ARG- 119	2.79	160.23	H-Bond (Protein Donor)	false
O8A	CZ	ARG- 119	3.77	0	Ionic (Protein Cationic)	false
O2A	N	GLY- 121	2.84	138.89	H-Bond (Protein Donor)	false
O4A	N	ALA- 123	2.9	159.27	H-Bond (Protein Donor)	false
CCP	CB	ALA- 123	3.7	0	Hydrophobic	false
O1A	OG1	THR- 124	2.56	162.01	H-Bond (Protein Donor)	false
O1A	N	THR- 124	2.74	159.06	H-Bond (Protein Donor)	false
S1P	CG1	VAL- 144	3.37	0	Hydrophobic	false
O5P	OD2	ASP- 147	2.94	142.27	H-Bond (Protein Donor)	false
S1P	CB	ASP- 147	4.18	0	Hydrophobic	false
O4A	O	HOH- 412	2.93	159.17	H-Bond (Protein Donor)	false