scPDB - 5byu entry

Protein Data Bank Entry:

PDB ID : 5byu

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2015-06-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thioesterase
ID:	Q5ZRL4_LEGPH
AC:	Q5ZRL4
Organism:	Legionella pneumophila subsp. pneumophila
Reign:	Bacteria
TaxID:	272624
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	59 %
B	41 %

Ligand binding site composition:

B-Factor:	39.198
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.164	675.000

% Hydrophobic	% Polar
50.50	49.50
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	47.97 %
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
-0.682188	-57.2275	-9.17065

Binding mode :

What is Poseview ?

2D View
3D View

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
S1P	CD1	LEU- 23	4.22	0	Hydrophobic	false
CDP	CG2	VAL- 57	4.06	0	Hydrophobic	false
C6P	CB	VAL- 57	3.48	0	Hydrophobic	false
S1P	CG1	VAL- 57	4.1	0	Hydrophobic	false
OAP	O	PHE- 65	3.26	162.27	H-Bond (Ligand Donor)	false
C6P	CB	PHE- 65	4.36	0	Hydrophobic	false
O9A	N	SER- 87	2.85	135.07	H-Bond (Protein Donor)	false
O3B	OG	SER- 88	3.03	134.54	H-Bond (Protein Donor)	false
O8A	OG	SER- 88	3.46	153.15	H-Bond (Protein Donor)	false
C4B	CB	SER- 88	3.62	0	Hydrophobic	false
N3A	NZ	LYS- 108	3.17	151.77	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 108	2.78	158.71	H-Bond (Protein Donor)	false
C1B	CD	LYS- 108	4.25	0	Hydrophobic	false
CDP	CG1	VAL- 110	4.02	0	Hydrophobic	false
C4B	CG2	VAL- 110	3.44	0	Hydrophobic	false
CDP	CG2	ILE- 112	3.63	0	Hydrophobic	false
CEP	CG2	ILE- 112	4.33	0	Hydrophobic	false
C5B	CB	SER- 119	4.17	0	Hydrophobic	false
O5A	N	SER- 119	2.76	161.44	H-Bond (Protein Donor)	false
O5A	OG	SER- 119	3.03	138.3	H-Bond (Protein Donor)	false