scPDB - 2vbq entry

Protein Data Bank Entry:

PDB ID : 2vbq

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-09-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminoglycoside N(6')-acetyltransferase type 1
ID:	AAC6_SALEN
AC:	Q9R381
Organism:	Salmonella enteritidis
Reign:	Bacteria
TaxID:	149539
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	15 %
B	85 %

Ligand binding site composition:

B-Factor:	19.921
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.088	1481.625

% Hydrophobic	% Polar
41.69	58.31
According to VolSite

Ligand :

HET Code:	BSJ
Formula:	C36H61N11O23P3S
Molecular weight:	1140.916 g/mol
DrugBank ID:	-
Buried Surface Area:	57.5 %
Polar Surface area:	624.33 Å2

Number of
H-Bond Acceptors:	29
H-Bond Donors:	12
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	3
Rule of Five Violation:	3
Rotatable Bonds:	25

Mass center Coordinates

X	Y	Z
25.7558	5.40738	36.5448

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
C48	CD1	LEU- 21	3.85	0	Hydrophobic	false
C65	CH2	TRP- 22	4.02	0	Hydrophobic	false
C63	CH2	TRP- 22	4.38	0	Hydrophobic	false
C60	CE2	TRP- 22	4.25	0	Hydrophobic	false
C59	CZ2	TRP- 22	4.21	0	Hydrophobic	false
C61	CZ2	TRP- 22	3.69	0	Hydrophobic	false
O53	NE1	TRP- 22	2.94	132.25	H-Bond (Protein Donor)	false
O55	NE2	HIS- 25	2.8	170.84	H-Bond (Protein Donor)	false
C63	CG	TYR- 66	4.06	0	Hydrophobic	false
C61	CZ	TYR- 66	3.88	0	Hydrophobic	false
C66	CE1	TYR- 66	3.81	0	Hydrophobic	false
N50	OH	TYR- 66	2.83	120.56	H-Bond (Ligand Donor)	false
C53	CD2	LEU- 78	4.43	0	Hydrophobic	false
C63	CB	GLU- 79	3.79	0	Hydrophobic	false
N52	OE1	GLU- 79	2.77	170.88	H-Bond (Ligand Donor)	false
N52	O	GLU- 79	2.78	171.64	H-Bond (Ligand Donor)	false
N52	OE1	GLU- 79	2.77	0	Ionic (Ligand Cationic)	false
O57	N	ILE- 81	2.95	149.18	H-Bond (Protein Donor)	false
C44	CG2	ILE- 81	3.99	0	Hydrophobic	false
C52	CG2	ILE- 81	3.8	0	Hydrophobic	false
C48	CD2	PHE- 82	3.94	0	Hydrophobic	false
O46	N	VAL- 83	2.87	169.44	H-Bond (Protein Donor)	false
C44	CG2	VAL- 83	4.21	0	Hydrophobic	false
C45	CD	ARG- 88	3.77	0	Hydrophobic	false
O32	N	GLN- 89	2.79	172.5	H-Bond (Protein Donor)	false
O23	N	GLY- 91	2.84	153.08	H-Bond (Protein Donor)	false
C44	CB	ALA- 93	4.09	0	Hydrophobic	false
C41	CB	ALA- 93	3.68	0	Hydrophobic	false
O31	N	ALA- 93	2.9	158.92	H-Bond (Protein Donor)	false
O22	N	LYS- 94	2.83	157.78	H-Bond (Protein Donor)	false
C15	CB	LYS- 94	4.47	0	Hydrophobic	false
O51	OD1	ASP- 115	2.85	144.76	H-Bond (Ligand Donor)	false
O52	OD1	ASP- 115	2.6	159.05	H-Bond (Ligand Donor)	false
S1	CB	THR- 116	3.51	0	Hydrophobic	false
O49	ND2	ASN- 120	2.88	163.97	H-Bond (Protein Donor)	false
S1	CB	SER- 123	3.66	0	Hydrophobic	false
C43	CG2	VAL- 126	3.9	0	Hydrophobic	false
C41	CG2	VAL- 126	4.02	0	Hydrophobic	false
C11	CG2	VAL- 126	4.3	0	Hydrophobic	false
C11	CB	ALA- 129	4.01	0	Hydrophobic	false
C14	CB	ALA- 129	3.7	0	Hydrophobic	false
C15	CD2	LEU- 130	3.63	0	Hydrophobic	false
N50	OE1	GLU- 136	3.04	132.41	H-Bond (Ligand Donor)	false
N50	OE2	GLU- 136	2.81	152.95	H-Bond (Ligand Donor)	false
N50	OE1	GLU- 136	3.04	0	Ionic (Ligand Cationic)	false
N50	OE2	GLU- 136	2.81	0	Ionic (Ligand Cationic)	false