scPDB - 5li5 entry

Protein Data Bank Entry:

PDB ID : 5li5

Resolution :2.790 Å

Experimental Method : X-ray

Deposition Date : 2016-07-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	KLTH0G14146p
ID:	C5DN49_LACTC
AC:	C5DN49
Organism:	Lachancea thermotolerans
Reign:	Eukaryota
TaxID:	559295
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.623
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.516	729.000

% Hydrophobic	% Polar
41.67	58.33
According to VolSite

Ligand :

HET Code:	THR_ALA_ASN_PRO_SEP
Formula:	C19H32N6O11P
Molecular weight:	551.465 g/mol
DrugBank ID:	-
Buried Surface Area:	44.18 %
Polar Surface area:	297.87 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	6
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-25.5908	16.7113	-4.83851

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
OD1	NZ	LYS- 51	2.6	125.78	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 58	2.66	161.35	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 58	3.51	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 132	3.8	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 132	3.21	0	Ionic (Protein Cationic)	false
O1P	NH2	ARG- 132	2.71	145.79	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 132	3.02	131.85	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 132	2.58	157.23	H-Bond (Protein Donor)	false
O1P	OH	TYR- 133	2.67	155.94	H-Bond (Protein Donor)	false
CB	CD2	LEU- 177	4.02	0	Hydrophobic	false
CG2	CG2	VAL- 181	3.54	0	Hydrophobic	false
CB	CG	GLU- 185	4.48	0	Hydrophobic	false
CB	CD1	ILE- 222	4.09	0	Hydrophobic	false
CB	CD2	LEU- 225	3.9	0	Hydrophobic	false
N	OD1	ASN- 229	3.02	160.91	H-Bond (Ligand Donor)	false
O	ND2	ASN- 229	2.91	162.28	H-Bond (Protein Donor)	false
CB	CD2	LEU- 232	4.47	0	Hydrophobic	false
OG1	NE1	TRP- 233	3.17	156.45	H-Bond (Protein Donor)	false
CG2	CZ2	TRP- 233	3.55	0	Hydrophobic	false