scPDB - 2prb entry

Protein Data Bank Entry:

PDB ID : 2prb

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-05-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminoglycoside 6-N-acetyltransferase type Ib11
ID:	Q8GLI5_SALTM
AC:	Q8GLI5
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	90371
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.538
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.110	988.875

% Hydrophobic	% Polar
42.66	57.34
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	53.83 %
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
-0.789854	5.6029	-14.3896

Binding mode :

What is Poseview ?

2D View
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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
C6P	CD1	ILE- 35	4.09	0	Hydrophobic	false
C6P	CB	TRP- 38	4.03	0	Hydrophobic	false
CEP	CG	GLN- 106	4.14	0	Hydrophobic	false
N4P	O	GLN- 106	3.01	126.75	H-Bond (Ligand Donor)	false
C6P	CB	LEU- 107	4.27	0	Hydrophobic	false
CEP	CG	LEU- 108	4.31	0	Hydrophobic	false
CAP	CD1	LEU- 108	4.39	0	Hydrophobic	false
O9P	N	LEU- 108	2.72	163.02	H-Bond (Protein Donor)	false
CAP	CD2	LEU- 114	3.77	0	Hydrophobic	false
O5A	N	GLY- 115	2.9	160.66	H-Bond (Protein Donor)	false
O1A	N	GLY- 117	2.84	148.8	H-Bond (Protein Donor)	false
O4A	N	GLY- 119	2.92	150.81	H-Bond (Protein Donor)	false
O2A	N	THR- 120	3.16	145.22	H-Bond (Protein Donor)	false
O2A	OG1	THR- 120	2.64	158.31	H-Bond (Protein Donor)	false
S1P	CB	PRO- 143	3.95	0	Hydrophobic	false
O5P	ND2	ASN- 147	3.07	172.6	H-Bond (Protein Donor)	false
C5B	CG	ARG- 149	4.16	0	Hydrophobic	false
CDP	CB	ALA- 150	3.88	0	Hydrophobic	false
S1P	CB	ALA- 150	4.13	0	Hydrophobic	false
O9A	NE	ARG- 152	3.38	161.26	H-Bond (Protein Donor)	false
O9A	CZ	ARG- 152	3.93	0	Ionic (Protein Cationic)	false
C4B	CG	ARG- 152	3.58	0	Hydrophobic	false
CCP	SG	CYS- 153	3.75	0	Hydrophobic	false
S1P	CE2	TYR- 154	4.37	0	Hydrophobic	false
O7A	NZ	LYS- 156	2.88	146.23	H-Bond (Protein Donor)	false
O5B	NZ	LYS- 156	3.08	165.3	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 156	2.88	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 156	3.93	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 156	3.37	0	Ionic (Protein Cationic)	false
C4B	CD	LYS- 156	4.26	0	Hydrophobic	false