scPDB - 3pn1 entry

Protein Data Bank Entry:

PDB ID : 3pn1

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-11-18

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:	24.023
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.604	853.875

% Hydrophobic	% Polar
44.27	55.73
According to VolSite

Ligand :

HET Code:	IVH
Formula:	C14H21N5O4S
Molecular weight:	355.413 g/mol
DrugBank ID:	-
Buried Surface Area:	60.68 %
Polar Surface area:	164.84 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
111.645	91.6091	27.6353

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
C1	CB	LEU- 80	4.15	0	Hydrophobic	false
C14	CB	SER- 81	4.41	0	Hydrophobic	false
S	CD1	LEU- 82	4.44	0	Hydrophobic	false
C2	CD2	LEU- 82	3.93	0	Hydrophobic	false
C3	CG	LEU- 82	4.28	0	Hydrophobic	false
C14	CD1	LEU- 82	3.7	0	Hydrophobic	false
N5	OE1	GLU- 114	2.68	152.99	H-Bond (Ligand Donor)	false
N5	O	PRO- 115	3.2	154.21	H-Bond (Ligand Donor)	false
N4	N	LEU- 117	3.05	132.91	H-Bond (Protein Donor)	false
C11	CB	ALA- 121	4.13	0	Hydrophobic	false
O4	OE1	GLU- 174	2.74	161.13	H-Bond (Ligand Donor)	false
O4	OE2	GLU- 174	3.49	121.74	H-Bond (Ligand Donor)	false
S	CD1	TYR- 226	3.92	0	Hydrophobic	false
C4	CE1	TYR- 226	3.65	0	Hydrophobic	false
C11	CZ	TYR- 226	3.93	0	Hydrophobic	false
DuAr	DuAr	TYR- 226	3.61	0	Aromatic Face/Face	false
N1	NZ	LYS- 291	3.06	155.99	H-Bond (Protein Donor)	false
C1	CG	PRO- 308	3.76	0	Hydrophobic	false