scPDB - 3bac entry

Protein Data Bank Entry:

PDB ID : 3bac

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2007-11-07

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_HAEIN
AC:	P43813
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	45.886
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.378	2224.125

% Hydrophobic	% Polar
45.98	54.02
According to VolSite

Ligand :

HET Code:	3B9
Formula:	C24H24N6O2
Molecular weight:	428.486 g/mol
DrugBank ID:	DB07041
Buried Surface Area:	49.39 %
Polar Surface area:	129.04 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
96.9907	108.524	77.4809

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
C17	CG2	ILE- 77	3.84	0	Hydrophobic	false
C24	CG2	ILE- 77	3.82	0	Hydrophobic	false
C17	CG	PRO- 78	3.83	0	Hydrophobic	false
C21	CG	PRO- 78	3.61	0	Hydrophobic	false
C11	CB	LEU- 80	4.31	0	Hydrophobic	false
C20	CD2	LEU- 80	4.23	0	Hydrophobic	false
C18	CD2	LEU- 80	3.63	0	Hydrophobic	false
O1	N	LEU- 80	3.32	126.14	H-Bond (Protein Donor)	false
C5	CD1	LEU- 82	3.84	0	Hydrophobic	false
C11	CD2	LEU- 82	3.45	0	Hydrophobic	false
N4	OE2	GLU- 114	3.01	157.14	H-Bond (Ligand Donor)	false
N4	O	PRO- 115	3.42	151.99	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 226	3.75	0	Aromatic Face/Face	false
C4	CG2	VAL- 289	4.1	0	Hydrophobic	false
N3	NZ	LYS- 291	3.44	147.91	H-Bond (Protein Donor)	false