scPDB - 4pu2 entry

Protein Data Bank Entry:

PDB ID : 4pu2

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2014-03-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminopeptidase N
ID:	Q9JYV4_NEIMB
AC:	Q9JYV4
Organism:	Neisseria meningitidis serogroup B
Reign:	Bacteria
TaxID:	122586
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.542
Number of residues:	28
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.008	1245.375

% Hydrophobic	% Polar
39.84	60.16
According to VolSite

Ligand :

HET Code:	PLU
Formula:	C5H13NO3P
Molecular weight:	166.135 g/mol
DrugBank ID:	DB02386
Buried Surface Area:	77.91 %
Polar Surface area:	100.64 Å2

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

Mass center Coordinates

X	Y	Z
11.5146	-43.9375	23.2187

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
CG	CB	GLU- 117	4.43	0	Hydrophobic	false
CD2	CG	GLU- 117	4.19	0	Hydrophobic	false
N	OE2	GLU- 117	3.58	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 117	2.77	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 117	2.77	130.84	H-Bond (Ligand Donor)	false
CD1	CZ	PHE- 254	4.48	0	Hydrophobic	false
CD2	CG	MET- 256	3.84	0	Hydrophobic	false
CD1	CG	MET- 256	3.59	0	Hydrophobic	false
CG	SD	MET- 259	3.51	0	Hydrophobic	false
N	OE2	GLU- 260	3.41	147.65	H-Bond (Ligand Donor)	false
N	OE1	GLU- 260	2.82	152.78	H-Bond (Ligand Donor)	false
N	OE2	GLU- 260	3.41	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 260	2.82	0	Ionic (Ligand Cationic)	false
O2	OE2	GLU- 294	3.3	147.21	H-Bond (Protein Donor)	false
O3	OE2	GLU- 294	2.79	143.5	H-Bond (Protein Donor)	false
N	OE2	GLU- 316	2.96	151.39	H-Bond (Ligand Donor)	false
N	OE2	GLU- 316	2.96	0	Ionic (Ligand Cationic)	false
CB	CE2	TYR- 372	4.41	0	Hydrophobic	false
CD2	CE2	TYR- 372	3.65	0	Hydrophobic	false
O1	ZN	ZN- 904	2.27	0	Metal Acceptor	false
O3	ZN	ZN- 904	2.12	0	Metal Acceptor	false