scPDB - 3e3u entry

Protein Data Bank Entry:

PDB ID : 3e3u

Resolution :1.560 Å

Experimental Method : X-ray

Deposition Date : 2008-08-08

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_MYCTU
AC:	P9WIJ3
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	3.5.1.88

Chains:

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

Ligand binding site composition:

B-Factor:	13.362
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.499	371.250

% Hydrophobic	% Polar
42.73	57.27
According to VolSite

Ligand :

HET Code:	NVC
Formula:	C19H25N3O4
Molecular weight:	359.419 g/mol
DrugBank ID:	DB08310
Buried Surface Area:	61.54 %
Polar Surface area:	86.88 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
20.6635	54.9896	17.2134

Binding mode :

What is Poseview ?

2D View
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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
O28	N	VAL- 50	2.85	167.63	H-Bond (Protein Donor)	false
C7	CG1	VAL- 50	3.63	0	Hydrophobic	false
C46	CG2	VAL- 50	3.88	0	Hydrophobic	false
O35	NE2	GLN- 56	3.05	147.74	H-Bond (Protein Donor)	false
C29	CG	LEU- 107	4.5	0	Hydrophobic	false
O35	N	LEU- 107	2.83	158.72	H-Bond (Protein Donor)	false
C49	CD1	LEU- 141	3.94	0	Hydrophobic	false
C13	CD1	LEU- 141	3.71	0	Hydrophobic	false
C11	CD2	LEU- 141	3.8	0	Hydrophobic	false
C49	CG	ARG- 144	3.86	0	Hydrophobic	false
C46	CB	MET- 145	4.21	0	Hydrophobic	false
C46	CB	HIS- 148	4.23	0	Hydrophobic	false
O39	OE1	GLU- 149	2.67	155.55	H-Bond (Protein Donor)	false
C24	CD1	PHE- 195	3.75	0	Hydrophobic	false
C21	CZ	PHE- 195	3.68	0	Hydrophobic	false