scPDB - 4q4e entry

Protein Data Bank Entry:

PDB ID : 4q4e

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2014-04-14

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:	15.779
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.213	590.625

% Hydrophobic	% Polar
36.00	64.00
According to VolSite

Ligand :

HET Code:	BB2
Formula:	C19H35N3O5
Molecular weight:	385.498 g/mol
DrugBank ID:	DB04310
Buried Surface Area:	58.33 %
Polar Surface area:	118.97 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
39.806	-37.8667	-33.6123

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
C17	CE	MET- 260	4.41	0	Hydrophobic	false
O13	N	GLY- 261	2.85	163.12	H-Bond (Protein Donor)	false
N1	O	ALA- 262	3.12	158.52	H-Bond (Ligand Donor)	false
C11	CG	ARG- 293	4.36	0	Hydrophobic	false
C8	CG2	VAL- 294	4.13	0	Hydrophobic	false
C11	CG2	VAL- 294	4.11	0	Hydrophobic	false
C11	CB	HIS- 297	3.93	0	Hydrophobic	false
O2	OE1	GLU- 298	2.74	142.52	H-Bond (Protein Donor)	false
C5	CZ	TYR- 381	4.35	0	Hydrophobic	false
C6	CE2	TYR- 381	4.02	0	Hydrophobic	false
C17	CE1	TYR- 381	4.13	0	Hydrophobic	false
O4	OH	TYR- 381	2.67	163.54	H-Bond (Protein Donor)	false
C24	CD	ARG- 783	3.85	0	Hydrophobic	false
O4	ZN	ZN- 901	2.05	0	Metal Acceptor	false
O2	ZN	ZN- 901	2.21	0	Metal Acceptor	false