scPDB - 3kr5 entry

Protein Data Bank Entry:

PDB ID : 3kr5

Resolution :2.560 Å

Experimental Method : X-ray

Deposition Date : 2009-11-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	M17 leucyl aminopeptidase
ID:	Q8IL11_PLAF7
AC:	Q8IL11
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	98 %
E	2 %

Ligand binding site composition:

B-Factor:	23.456
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.701	688.500

% Hydrophobic	% Polar
44.61	55.39
According to VolSite

Ligand :

HET Code:	BEY
Formula:	C19H23NO4P
Molecular weight:	360.364 g/mol
DrugBank ID:	DB07448
Buried Surface Area:	61.85 %
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
100.641	61.5088	11.1359

Binding mode :

What is Poseview ?

2D View
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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
C12	CE	MET- 392	3.37	0	Hydrophobic	false
C18	CE	MET- 396	3.69	0	Hydrophobic	false
C10	CE	MET- 396	3.56	0	Hydrophobic	false
N	OD1	ASP- 399	3.33	142.77	H-Bond (Ligand Donor)	false
N	OD1	ASP- 399	3.33	0	Ionic (Ligand Cationic)	false
C4	CB	ASN- 457	4.2	0	Hydrophobic	false
C2	CB	ASP- 459	4.19	0	Hydrophobic	false
C1	CB	ALA- 460	4.08	0	Hydrophobic	false
C5	CB	ALA- 460	4.07	0	Hydrophobic	false
O1	N	GLY- 489	2.74	156.24	H-Bond (Protein Donor)	false
C12	CD1	LEU- 492	3.57	0	Hydrophobic	false
C6	CG2	ILE- 547	3.9	0	Hydrophobic	false
C15	CB	ALA- 577	4.32	0	Hydrophobic	false
C13	CB	ALA- 577	3.8	0	Hydrophobic	false
O4	ZN	ZN- 1001	2.06	0	Metal Acceptor	false
O3	ZN	ZN- 1004	2.49	0	Metal Acceptor	false
O4	ZN	ZN- 1004	2.37	0	Metal Acceptor	false