scPDB - 5byl entry

Protein Data Bank Entry:

PDB ID : 5byl

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2015-06-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional AAC/APH
ID:	AACA_STAAU
AC:	P0A0C1
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	2.3.1

Chains:

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

Ligand binding site composition:

B-Factor:	41.407
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.439	735.750

% Hydrophobic	% Polar
42.20	57.80
According to VolSite

Ligand :

HET Code:	GCP
Formula:	C11H14N5O13P3
Molecular weight:	517.176 g/mol
DrugBank ID:	DB03725
Buried Surface Area:	55.49 %
Polar Surface area:	326.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
46.5725	-3.56591	55.3353

Binding mode :

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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
C1'	CD1	ILE- 208	3.46	0	Hydrophobic	false
O1B	OG	SER- 214	3.21	145.34	H-Bond (Protein Donor)	false
C5'	CB	ALA- 216	3.83	0	Hydrophobic	false
O1B	NZ	LYS- 226	3.69	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 226	3.07	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 226	2.71	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 226	3.07	137.42	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 226	2.71	140.1	H-Bond (Protein Donor)	false
N7	OH	TYR- 274	2.62	140.61	H-Bond (Protein Donor)	false
O6	N	ILE- 277	2.84	162.17	H-Bond (Protein Donor)	false
N1	O	ILE- 277	2.78	160.21	H-Bond (Ligand Donor)	false
N2	O	ILE- 277	3.08	139.99	H-Bond (Ligand Donor)	false
C2'	CZ	PHE- 281	3.81	0	Hydrophobic	false
C3'	CD1	ILE- 392	3.74	0	Hydrophobic	false
O2A	MG	MG- 700	1.88	0	Metal Acceptor	false
O3G	MG	MG- 702	1.98	0	Metal Acceptor	false
O2B	MG	MG- 702	2.07	0	Metal Acceptor	false
O1A	O	HOH- 906	2.81	171.72	H-Bond (Protein Donor)	false