scPDB - 2zxg entry

Protein Data Bank Entry:

PDB ID : 2zxg

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2008-12-24

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:	AMPN_ECOLI
AC:	P04825
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.4.11.2

Chains:

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

Ligand binding site composition:

B-Factor:	11.981
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.941	1323.000

% Hydrophobic	% Polar
30.87	69.13
According to VolSite

Ligand :

HET Code:	S23
Formula:	C21H26N2O5P
Molecular weight:	417.415 g/mol
DrugBank ID:	DB08506
Buried Surface Area:	63.63 %
Polar Surface area:	146.81 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
73.3862	49.4489	6.13921

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
N1	OE2	GLU- 121	2.78	168.19	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 121	2.78	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 121	3.91	0	Ionic (Ligand Cationic)	false
C2	SD	MET- 260	3.4	0	Hydrophobic	false
C3	SD	MET- 260	4.25	0	Hydrophobic	false
C21	CB	MET- 260	3.49	0	Hydrophobic	false
O3	N	GLY- 261	2.95	152.95	H-Bond (Protein Donor)	false
C2	SD	MET- 263	4.43	0	Hydrophobic	false
N1	OE2	GLU- 264	2.69	151	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 264	3.32	122.11	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 264	2.69	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 264	3.32	0	Ionic (Ligand Cationic)	false
C6	CG1	VAL- 294	4.33	0	Hydrophobic	false
C11	CG2	VAL- 294	3.46	0	Hydrophobic	false
C8	CB	HIS- 297	4.06	0	Hydrophobic	false
O2	OE2	GLU- 298	2.61	160.97	H-Bond (Protein Donor)	false
N1	OE1	GLU- 320	3.13	160.61	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 320	3.13	0	Ionic (Ligand Cationic)	false
C2	CE2	TYR- 376	3.85	0	Hydrophobic	false
C20	CB	TYR- 376	3.49	0	Hydrophobic	false
O1	OH	TYR- 381	2.69	157.35	H-Bond (Protein Donor)	false
C4	CE2	TYR- 381	4.2	0	Hydrophobic	false
C19	CD	ARG- 825	4.35	0	Hydrophobic	false
O1	ZN	ZN- 900	2.01	0	Metal Acceptor	false