scPDB - 1soz entry

Protein Data Bank Entry:

PDB ID : 1soz

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2004-03-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine endoprotease DegS
ID:	DEGS_ECOLI
AC:	P0AEE3
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.4.21.107

Chains:

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

Ligand binding site composition:

B-Factor:	99.999
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.283	1488.375

% Hydrophobic	% Polar
54.20	45.80
According to VolSite

Ligand :

HET Code:	VAL_TYR_GLN_PHE
Formula:	C28H37N5O7
Molecular weight:	555.623 g/mol
DrugBank ID:	-
Buried Surface Area:	36.37 %
Polar Surface area:	218.38 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	6
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
21.3189	50.473	18.5949

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
CE1	CD1	ILE- 259	4.43	0	Hydrophobic	false
CZ	CD1	ILE- 261	3.74	0	Hydrophobic	false
O	N	GLY- 263	3.06	151.83	H-Bond (Protein Donor)	false
CG2	CB	ARG- 264	3.38	0	Hydrophobic	false
OH	O	VAL- 283	2.83	149.63	H-Bond (Ligand Donor)	false
CD2	CB	ALA- 315	3.67	0	Hydrophobic	false
CZ	CG2	THR- 318	3.34	0	Hydrophobic	false
CB	CE	MET- 319	4.24	0	Hydrophobic	false
CB	CB	MET- 319	3.32	0	Hydrophobic	false
CD1	CB	VAL- 322	4.09	0	Hydrophobic	false
CE1	CG2	VAL- 322	3.52	0	Hydrophobic	false