scPDB - 4eox entry

Protein Data Bank Entry:

PDB ID : 4eox

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2012-04-16

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:	DEF_STRR6
AC:	Q8DP79
Organism:	Streptococcus pneumoniae
Reign:	Bacteria
TaxID:	171101
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.150
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.317	283.500

% Hydrophobic	% Polar
39.29	60.71
According to VolSite

Ligand :

HET Code:	0S5
Formula:	C22H29N3O5
Molecular weight:	415.483 g/mol
DrugBank ID:	-
Buried Surface Area:	61.5 %
Polar Surface area:	107.02 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
24.0106	-5.67893	4.89473

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
C25	CG	GLN- 57	4.06	0	Hydrophobic	false
N20	O	GLY- 69	3.01	163.16	H-Bond (Ligand Donor)	false
O12	N	VAL- 71	2.8	161.37	H-Bond (Protein Donor)	false
C24	CG1	VAL- 71	3.62	0	Hydrophobic	false
C6	CG2	VAL- 71	3.89	0	Hydrophobic	false
O1	NE2	GLN- 77	3.45	144.68	H-Bond (Protein Donor)	false
C25	CG	PRO- 90	4.34	0	Hydrophobic	false
C8	CD1	LEU- 124	4.16	0	Hydrophobic	false
C8	CG	GLU- 128	3.92	0	Hydrophobic	false
C7	CB	GLU- 128	4.47	0	Hydrophobic	false
C15	CD2	LEU- 131	4.42	0	Hydrophobic	false
O1	N	LEU- 131	2.75	159.2	H-Bond (Protein Donor)	false
C9	CG2	ILE- 169	4.24	0	Hydrophobic	false
C10	CG2	VAL- 170	3.88	0	Hydrophobic	false
C10	CB	HIS- 173	3.97	0	Hydrophobic	false