scPDB - 4k5p entry

Protein Data Bank Entry:

PDB ID : 4k5p

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2013-04-15

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:	16.878
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.691	847.125

% Hydrophobic	% Polar
40.24	59.76
According to VolSite

Ligand :

HET Code:	1OS
Formula:	C8H12N3O3P
Molecular weight:	229.173 g/mol
DrugBank ID:	-
Buried Surface Area:	72.93 %
Polar Surface area:	152.25 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
12.6003	11.9594	14.3833

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
N3	OE2	GLU- 319	3.41	138.64	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 319	2.61	165.47	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 319	3.41	0	Ionic (Ligand Cationic)	false
N3	OE1	GLU- 319	2.61	0	Ionic (Ligand Cationic)	false
C4	CG	GLU- 319	4.41	0	Hydrophobic	false
C8	CG2	VAL- 459	3.58	0	Hydrophobic	false
C7	SD	MET- 462	3.34	0	Hydrophobic	false
N3	OE2	GLU- 463	3.9	0	Ionic (Ligand Cationic)	false
N3	OE1	GLU- 463	3.33	0	Ionic (Ligand Cationic)	false
O1	OE1	GLU- 497	2.74	159.45	H-Bond (Protein Donor)	false
N3	OE2	GLU- 519	2.82	0	Ionic (Ligand Cationic)	false
C3	CD1	TYR- 575	3.23	0	Hydrophobic	false
O2	OH	TYR- 580	2.55	153.35	H-Bond (Protein Donor)	false
O1	ZN	ZN- 1101	2.34	0	Metal Acceptor	false
O2	ZN	ZN- 1101	1.89	0	Metal Acceptor	false