scPDB - 5azg entry

Protein Data Bank Entry:

PDB ID : 5azg

Resolution :1.810 Å

Experimental Method : X-ray

Deposition Date : 2015-10-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein lgg-1
ID:	LGG1_CAEEL
AC:	Q09490
Organism:	Caenorhabditis elegans
Reign:	Eukaryota
TaxID:	6239
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	85 %
B	15 %
D	0 %

Ligand binding site composition:

B-Factor:	36.739
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.740	850.500

% Hydrophobic	% Polar
51.98	48.02
According to VolSite

Ligand :

HET Code:	ASP_PHE_THR_PHE_LEU
Formula:	C32H42N5O9
Molecular weight:	640.704 g/mol
DrugBank ID:	-
Buried Surface Area:	45.87 %
Polar Surface area:	244.52 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
10.9992	26.4648	20.4157

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
CZ	CG	GLU- 17	4.43	0	Hydrophobic	false
CD1	CD1	ILE- 21	3.51	0	Hydrophobic	false
CZ	CG1	ILE- 21	3.88	0	Hydrophobic	false
OXT	NH1	ARG- 28	2.7	171.71	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 28	3.62	0	Ionic (Protein Cationic)	false
CD2	CD	ARG- 28	3.71	0	Hydrophobic	false
CE2	CB	PRO- 30	4.23	0	Hydrophobic	false
N	O	LYS- 48	3.02	169.29	H-Bond (Ligand Donor)	false
CZ	CD	LYS- 48	4.22	0	Hydrophobic	false
CD2	CB	LYS- 48	3.74	0	Hydrophobic	false
CB	CD2	TYR- 49	3.72	0	Hydrophobic	false
CG	CD2	TYR- 49	3.63	0	Hydrophobic	false
CB	CD1	LEU- 50	3.65	0	Hydrophobic	false
CD2	CB	LEU- 50	4.42	0	Hydrophobic	false
CD2	CG	LEU- 50	3.82	0	Hydrophobic	false
CZ	CD1	LEU- 50	3.65	0	Hydrophobic	false
O	N	LEU- 50	2.82	164.44	H-Bond (Protein Donor)	false
N	O	LEU- 50	3.19	172.25	H-Bond (Ligand Donor)	false
CD1	CG1	VAL- 51	3.91	0	Hydrophobic	false
CD1	CE1	PHE- 60	3.59	0	Hydrophobic	false
CB	CD1	LEU- 63	4.32	0	Hydrophobic	false
CD1	CD1	LEU- 63	4.47	0	Hydrophobic	false
CD2	CD2	LEU- 63	3.97	0	Hydrophobic	false
CD1	CD	LYS- 66	4.19	0	Hydrophobic	false