scPDB - 2kmn entry

Protein Data Bank Entry:

PDB ID : 2kmn

Resolution : Å

Experimental Method : NMR

Deposition Date : 2009-08-01

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_ECOLI
AC:	P0A6K3
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.5.1.88

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.233	354.375

% Hydrophobic	% Polar
47.62	52.38
According to VolSite

Ligand :

HET Code:	BB2
Formula:	C19H35N3O5
Molecular weight:	385.498 g/mol
DrugBank ID:	DB04310
Buried Surface Area:	70.78 %
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
253.436	7.87507	4.58696

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
O13	N	ILE- 44	2.9	123.66	H-Bond (Protein Donor)	false
C24	CD1	ILE- 44	4	0	Hydrophobic	false
C25	CG1	ILE- 44	3.62	0	Hydrophobic	false
O4	NE2	GLN- 50	2.78	163.27	H-Bond (Protein Donor)	false
C10	CG2	ILE- 60	4.4	0	Hydrophobic	false
C11	CB	ILE- 60	3.41	0	Hydrophobic	false
C9	CG2	VAL- 62	4.25	0	Hydrophobic	false
N14	O	GLY- 89	2.79	124.97	H-Bond (Ligand Donor)	false
O20	N	GLY- 89	3.02	126.32	H-Bond (Protein Donor)	false
C5	SG	CYS- 90	4.06	0	Hydrophobic	false
O4	N	LEU- 91	3.15	145.74	H-Bond (Protein Donor)	false
C17	CG	LEU- 91	3.56	0	Hydrophobic	false
C16	CD1	LEU- 91	4.1	0	Hydrophobic	false
C24	CD	ARG- 97	4.43	0	Hydrophobic	false
C9	CB	CYS- 129	3.32	0	Hydrophobic	false
C10	CB	CYS- 129	3.56	0	Hydrophobic	false
O2	OE1	GLU- 133	2.66	162.75	H-Bond (Protein Donor)	false
C9	CG	GLU- 133	4.44	0	Hydrophobic	false
C11	CG	GLU- 133	3.41	0	Hydrophobic	false
O4	ZN	ZN- 148	2.35	0	Metal Acceptor	false
O2	ZN	ZN- 148	2.34	0	Metal Acceptor	false