scPDB - 2ek9 entry

Protein Data Bank Entry:

PDB ID : 2ek9

Resolution :1.970 Å

Experimental Method : X-ray

Deposition Date : 2007-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminopeptidase
ID:	A2V759_9BACL
AC:	A2V759
Organism:	Aneurinibacillus sp. AM-1
Reign:	Bacteria
TaxID:	400761
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.971
Number of residues:	28
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.132	344.250

% Hydrophobic	% Polar
52.94	47.06
According to VolSite

Ligand :

HET Code:	BES
Formula:	C16H24N2O4
Molecular weight:	308.373 g/mol
DrugBank ID:	DB03424
Buried Surface Area:	60.41 %
Polar Surface area:	117.1 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
14.9636	19.3429	18.0355

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
O2	NE2	HIS- 228	3.26	129.13	H-Bond (Ligand Donor)	false
O2	OE1	GLU- 272	3.38	143.52	H-Bond (Ligand Donor)	false
C14	CD2	LEU- 276	4.05	0	Hydrophobic	false
C15	CG	LEU- 276	4.17	0	Hydrophobic	false
C8	SD	MET- 302	4.28	0	Hydrophobic	false
C11	CG	GLU- 343	4.4	0	Hydrophobic	false
N1	O	ARG- 345	2.68	169.78	H-Bond (Ligand Donor)	false
C13	CB	ARG- 345	3.6	0	Hydrophobic	false
C12	CB	ARG- 345	3.68	0	Hydrophobic	false
O1	NH2	ARG- 345	3.08	140.21	H-Bond (Protein Donor)	false
O1	NE	ARG- 345	2.88	154.32	H-Bond (Protein Donor)	false
O1	CZ	ARG- 345	3.41	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 345	3.75	166.26	Pi/Cation	false
C12	CD2	LEU- 360	4.28	0	Hydrophobic	false
C11	CD1	ILE- 362	3.6	0	Hydrophobic	false
C10	CD1	ILE- 362	3.61	0	Hydrophobic	false
C9	CG1	VAL- 366	3.73	0	Hydrophobic	false
O3	OH	TYR- 370	3.32	161.34	H-Bond (Protein Donor)	false
O2	ZN	ZN- 1001	2.12	0	Metal Acceptor	false
O3	ZN	ZN- 1001	2.2	0	Metal Acceptor	false