scPDB - 4glx entry

Protein Data Bank Entry:

PDB ID : 4glx

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-08-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA ligase
ID:	DNLJ_ECOLI
AC:	P15042
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.5.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	12.059
Number of residues:	29
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.834	1177.875

% Hydrophobic	% Polar
40.11	59.89
According to VolSite

Ligand :

HET Code:	0XS
Formula:	C10H6BrF3N4O
Molecular weight:	335.080 g/mol
DrugBank ID:	-
Buried Surface Area:	67.85 %
Polar Surface area:	94.88 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
27.4699	4.21658	5.37547

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
F9	CD2	LEU- 82	3.81	0	Hydrophobic	false
C4	CD1	LEU- 82	3.84	0	Hydrophobic	false
C2	CG	LEU- 82	3.94	0	Hydrophobic	false
N17	OE2	GLU- 113	3.09	162.79	H-Bond (Ligand Donor)	false
N17	O	LEU- 114	3.21	134.37	H-Bond (Ligand Donor)	false
C14	CG	LYS- 115	4.47	0	Hydrophobic	false
O18	N	LEU- 116	3.01	146.9	H-Bond (Protein Donor)	false
N19	O	LEU- 116	3.31	173.27	H-Bond (Ligand Donor)	false
C14	CB	TYR- 225	4.46	0	Hydrophobic	false
F10	CE1	TYR- 225	4.26	0	Hydrophobic	false
DuAr	DuAr	TYR- 225	3.57	0	Aromatic Face/Face	false
DuAr	DuAr	TYR- 225	3.85	0	Aromatic Face/Face	false
C14	CG2	VAL- 288	3.87	0	Hydrophobic	false
N13	NZ	LYS- 290	2.95	170.19	H-Bond (Protein Donor)	false
N5	NZ	LYS- 290	3	123.65	H-Bond (Protein Donor)	false
F11	CD	LYS- 290	3.62	0	Hydrophobic	false
F9	CG	PRO- 307	3.59	0	Hydrophobic	false
F11	CZ3	TRP- 309	3.3	0	Hydrophobic	false
F9	CH2	TRP- 309	3.65	0	Hydrophobic	false
F11	CB	ALA- 310	4.36	0	Hydrophobic	false
N19	O	HOH- 778	3.45	131.71	H-Bond (Ligand Donor)	false
N19	O	HOH- 846	3.47	123.15	H-Bond (Ligand Donor)	false