scPDB - 4je7 entry

Protein Data Bank Entry:

PDB ID : 4je7

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2013-02-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptide deformylase 1A, chloroplastic/mitochondrial
ID:	DEF1A_ARATH
AC:	Q9FV53
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	3.5.1.88

Chains:

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

Ligand binding site composition:

B-Factor:	19.991
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.236	799.875

% Hydrophobic	% Polar
39.24	60.76
According to VolSite

Ligand :

HET Code:	BB2
Formula:	C19H35N3O5
Molecular weight:	385.498 g/mol
DrugBank ID:	DB04310
Buried Surface Area:	65.87 %
Polar Surface area:	118.97 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
29.7374	-17.0833	-35.7561

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
C5	CB	CYS- 47	3.69	0	Hydrophobic	false
O13	N	VAL- 48	3.12	162.05	H-Bond (Protein Donor)	false
C7	CG2	VAL- 48	3.97	0	Hydrophobic	false
C9	CG2	VAL- 48	4.12	0	Hydrophobic	false
C25	CG1	VAL- 48	3.72	0	Hydrophobic	false
N1	O	GLY- 49	3.09	122.07	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 54	3.18	161.89	H-Bond (Protein Donor)	false
O2	NE2	GLN- 54	3.32	122.28	H-Bond (Protein Donor)	false
C25	CB	TYR- 70	4.04	0	Hydrophobic	false
C10	CG	GLU- 109	3.72	0	Hydrophobic	false
N14	O	GLY- 110	3.41	155.28	H-Bond (Ligand Donor)	false
C5	CG	GLU- 112	3.97	0	Hydrophobic	false
O4	N	GLU- 112	2.78	150.68	H-Bond (Protein Donor)	false
C11	CZ2	TRP- 146	3.53	0	Hydrophobic	false
C10	CG	ARG- 149	3.81	0	Hydrophobic	false
C11	CD	ARG- 149	3.47	0	Hydrophobic	false
C9	CG1	ILE- 150	3.99	0	Hydrophobic	false
C9	CB	HIS- 153	3.9	0	Hydrophobic	false
O2	OE1	GLU- 154	2.62	132.56	H-Bond (Protein Donor)	false
O4	ZN	ZN- 202	2.24	0	Metal Acceptor	false
O2	ZN	ZN- 202	2.32	0	Metal Acceptor	false