scPDB - 3h8g entry

Protein Data Bank Entry:

PDB ID : 3h8g

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2009-04-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytosol aminopeptidase
ID:	AMPA_PSEPU
AC:	O86436
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	3.4.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	8.104
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN MN

Cavity properties

Ligandability	Volume (Å3)
0.429	658.125

% Hydrophobic	% Polar
37.44	62.56
According to VolSite

Ligand :

HET Code:	BES
Formula:	C16H24N2O4
Molecular weight:	308.373 g/mol
DrugBank ID:	DB03424
Buried Surface Area:	59.54 %
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
-25.544	-19.9432	-7.49595

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	NZ	LYS- 279	2.85	145.33	H-Bond (Protein Donor)	false
C1	SD	MET- 287	4.42	0	Hydrophobic	false
C10	CE	MET- 287	3.67	0	Hydrophobic	false
C15	CB	ASN- 347	4.39	0	Hydrophobic	false
C15	CB	ASP- 349	4.46	0	Hydrophobic	false
C16	CB	ALA- 350	4.2	0	Hydrophobic	false
C15	CB	ALA- 350	4.12	0	Hydrophobic	false
N2	O	THR- 376	3.07	163.73	H-Bond (Ligand Donor)	false
N1	O	LEU- 377	3.36	149.86	H-Bond (Ligand Donor)	false
O1	N	GLY- 379	2.9	155.27	H-Bond (Protein Donor)	false
C11	CD1	ILE- 382	3.84	0	Hydrophobic	false
C15	CG2	ILE- 437	4.5	0	Hydrophobic	false
C16	CG2	ILE- 437	3.72	0	Hydrophobic	false
C12	CB	ALA- 466	3.7	0	Hydrophobic	false
C11	CH2	TRP- 470	3.29	0	Hydrophobic	false
O2	ZN	ZN- 501	2.07	0	Metal Acceptor	false
O2	MN	MN- 502	2.19	0	Metal Acceptor	false
O3	MN	MN- 502	2.45	0	Metal Acceptor	false