scPDB - 3ebi entry

Protein Data Bank Entry:

PDB ID : 3ebi

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-08-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	M1 family aminopeptidase
ID:	AMP1_PLAFQ
AC:	O96935
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	186763
EC Number:	3.4.11

Chains:

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

Ligand binding site composition:

B-Factor:	12.876
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.139	617.625

% Hydrophobic	% Polar
42.62	57.38
According to VolSite

Ligand :

HET Code:	BEY
Formula:	C19H23NO4P
Molecular weight:	360.364 g/mol
DrugBank ID:	DB07448
Buried Surface Area:	69.47 %
Polar Surface area:	117.71 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
14.9546	10.772	12.6001

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
O3	ZN	ZN- 1	1.86	0	Metal Acceptor	false
C11	CG	GLN- 317	4.32	0	Hydrophobic	false
C13	CG	GLU- 319	3.85	0	Hydrophobic	false
C16	CB	GLU- 319	4.32	0	Hydrophobic	false
N	OE2	GLU- 319	3.86	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 319	2.53	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 319	2.53	132.38	H-Bond (Ligand Donor)	false
C17	CG2	VAL- 459	3.87	0	Hydrophobic	false
C15	CG2	VAL- 459	4.05	0	Hydrophobic	false
C10	CG2	VAL- 459	3.53	0	Hydrophobic	false
O1	N	GLY- 460	2.86	160.79	H-Bond (Protein Donor)	false
C15	SD	MET- 462	3.69	0	Hydrophobic	false
N	OE2	GLU- 463	3.4	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 463	2.59	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 463	2.59	129.97	H-Bond (Ligand Donor)	false
C6	CG2	VAL- 493	3.65	0	Hydrophobic	false
C3	CB	HIS- 496	3.68	0	Hydrophobic	false
O4	OE2	GLU- 497	2.74	152.86	H-Bond (Protein Donor)	false
N	OE2	GLU- 519	3.64	0	Ionic (Ligand Cationic)	false
C12	CG	GLU- 572	3.76	0	Hydrophobic	false
C18	CE1	TYR- 575	3.99	0	Hydrophobic	false
C13	CE1	TYR- 575	3.41	0	Hydrophobic	false
O3	OH	TYR- 580	2.79	156.17	H-Bond (Protein Donor)	false
C8	CE1	TYR- 580	4.27	0	Hydrophobic	false
C14	CE	MET- 1034	4.33	0	Hydrophobic	false
C12	SD	MET- 1034	3.59	0	Hydrophobic	false