scPDB - 5es7 entry

Protein Data Bank Entry:

PDB ID : 5es7

Resolution :2.810 Å

Experimental Method : X-ray

Deposition Date : 2015-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Linear gramicidin synthase subunit A
ID:	LGRA_BREPA
AC:	Q70LM7
Organism:	Brevibacillus parabrevis
Reign:	Bacteria
TaxID:	54914
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	99.999
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.204	837.000

% Hydrophobic	% Polar
54.84	45.16
According to VolSite

Ligand :

HET Code:	FON
Formula:	C20H21N7O7
Molecular weight:	471.423 g/mol
DrugBank ID:	DB03256
Buried Surface Area:	47.75 %
Polar Surface area:	221.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
179.097	30.9407	1.101

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
C7	CB	TYR- 53	3.96	0	Hydrophobic	false
N10	O	TYR- 53	3.1	136.69	H-Bond (Ligand Donor)	false
N8	O	TYR- 55	2.7	135.01	H-Bond (Ligand Donor)	false
C13	CG2	ILE- 56	3.63	0	Hydrophobic	false
N1	N	LEU- 57	3.14	137.37	H-Bond (Protein Donor)	false
NA2	O	LEU- 57	3.15	146.52	H-Bond (Ligand Donor)	false
C16	CD	ARG- 83	3.62	0	Hydrophobic	false
N3	O	ASP- 104	3.18	139.89	H-Bond (Ligand Donor)	false
C9	CG1	VAL- 107	4.06	0	Hydrophobic	false
O4	N	ASP- 108	3.08	161.5	H-Bond (Protein Donor)	false
CB	CD1	PHE- 166	4.43	0	Hydrophobic	false
O2	N	LYS- 167	2.77	166.39	H-Bond (Protein Donor)	false