scPDB - 3gdv entry

Protein Data Bank Entry:

PDB ID : 3gdv

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2009-02-24

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
C	100 %

Ligand binding site composition:

B-Factor:	70.603
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.979	556.875

% Hydrophobic	% Polar
47.88	52.12
According to VolSite

Ligand :

HET Code:	TYR_GLN_PHE
Formula:	C23H28N4O6
Molecular weight:	456.492 g/mol
DrugBank ID:	-
Buried Surface Area:	51.44 %
Polar Surface area:	189.28 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-14.9187	74.1758	6.72321

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
O	NH1	ARG- 186	2.88	143.47	H-Bond (Protein Donor)	false
O	N	ILE- 259	3.46	147.67	H-Bond (Protein Donor)	false
OXT	N	ILE- 259	2.91	158.55	H-Bond (Protein Donor)	false
CE2	CD1	ILE- 259	3.26	0	Hydrophobic	false
O	N	GLY- 260	2.86	129.68	H-Bond (Protein Donor)	false
N	O	ILE- 261	3.12	161.69	H-Bond (Ligand Donor)	false
O	N	ILE- 261	3.16	157.08	H-Bond (Protein Donor)	false
CZ	CG2	ILE- 261	4.11	0	Hydrophobic	false
N	O	GLY- 263	3.47	161.38	H-Bond (Ligand Donor)	false
O	N	GLY- 263	3	152.62	H-Bond (Protein Donor)	false
CZ	CD1	ILE- 282	4.47	0	Hydrophobic	false
NE2	OE1	GLU- 286	3.04	133.59	H-Bond (Ligand Donor)	false
CD1	CD2	LEU- 316	3.74	0	Hydrophobic	false
CE1	CD2	LEU- 316	3.85	0	Hydrophobic	false
CE2	CG2	THR- 318	4.15	0	Hydrophobic	false
CB	CE	MET- 319	3.98	0	Hydrophobic	false
CD1	CE	MET- 319	4.15	0	Hydrophobic	false
CB	CE	MET- 319	3.56	0	Hydrophobic	false
CD1	CE	MET- 319	3.85	0	Hydrophobic	false
CG	CB	MET- 319	3.95	0	Hydrophobic	false
CD2	CG2	VAL- 322	4.03	0	Hydrophobic	false