scPDB - 2ew6 entry

Protein Data Bank Entry:

PDB ID : 2ew6

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2005-11-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptide deformylase
ID:	Q672W7_HELPX
AC:	Q672W7
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	210
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.154
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.605	303.750

% Hydrophobic	% Polar
51.11	48.89
According to VolSite

Ligand :

HET Code:	Y13
Formula:	C17H17NO4
Molecular weight:	299.321 g/mol
DrugBank ID:	DB08754
Buried Surface Area:	63.88 %
Polar Surface area:	89.79 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-57.1141	-91.434	97.7257

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
C7	CG1	ILE- 45	4.45	0	Hydrophobic	false
C4	CD1	ILE- 45	3.59	0	Hydrophobic	false
O27	N	ILE- 45	2.68	155.91	H-Bond (Protein Donor)	false
O27	N	GLY- 46	3.35	160.38	H-Bond (Protein Donor)	false
C2	CG	GLU- 94	4.14	0	Hydrophobic	false
C1	CB	GLU- 94	3.57	0	Hydrophobic	false
C14	CD2	LEU- 97	3.55	0	Hydrophobic	false
O23	N	GLY- 101	2.78	152.45	H-Bond (Protein Donor)	false
C3	CD1	LEU- 131	3.54	0	Hydrophobic	false
C2	CG1	VAL- 134	3.78	0	Hydrophobic	false
C4	CB	ALA- 135	3.62	0	Hydrophobic	false