scPDB - 5kl9 entry

Protein Data Bank Entry:

PDB ID : 5kl9

Resolution :2.220 Å

Experimental Method : X-ray

Deposition Date : 2016-06-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-CoA thioester hydrolase YbgC
ID:	YBGC_ECO57
AC:	P0A8Z5
Organism:	Escherichia coli O157:H7
Reign:	Bacteria
TaxID:	83334
EC Number:	3.1.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	64 %
D	36 %

Ligand binding site composition:

B-Factor:	49.843
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.196	691.875

% Hydrophobic	% Polar
50.24	49.76
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	40.35 %
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
21.1694	14.1144	-12.3161

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
C2P	CG2	VAL- 22	4.26	0	Hydrophobic	false
C2P	CB	HIS- 25	3.9	0	Hydrophobic	false
CEP	CG2	VAL- 58	3.78	0	Hydrophobic	false
C6P	CB	VAL- 58	4.13	0	Hydrophobic	false
S1P	CB	VAL- 58	3.89	0	Hydrophobic	false
N4P	O	VAL- 59	3.21	159.22	H-Bond (Ligand Donor)	false
S1P	CG2	VAL- 59	4.28	0	Hydrophobic	false
O1A	CZ	ARG- 60	3.41	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 60	3.23	132.99	H-Bond (Protein Donor)	false
O1A	NE	ARG- 60	2.73	165.3	H-Bond (Protein Donor)	false
CCP	CD	ARG- 60	4.22	0	Hydrophobic	false
CEP	CD	ARG- 60	4.1	0	Hydrophobic	false
N8P	O	TYR- 66	3.35	153.34	H-Bond (Ligand Donor)	false
C6P	CB	TYR- 66	4.23	0	Hydrophobic	false
C1B	CB	TYR- 67	4.28	0	Hydrophobic	false
C4B	CD1	TYR- 67	3.55	0	Hydrophobic	false
CEP	CB	VAL- 112	4.26	0	Hydrophobic	false
CDP	CG1	VAL- 114	4	0	Hydrophobic	false
CCP	CG	PRO- 121	4.2	0	Hydrophobic	false
CDP	CG	PRO- 121	3.82	0	Hydrophobic	false