scPDB - 1g27 entry

Protein Data Bank Entry:

PDB ID : 1g27

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2000-10-17

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
C	100 %

Ligand binding site composition:

B-Factor:	39.216
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.342	435.375

% Hydrophobic	% Polar
34.11	65.89
According to VolSite

Ligand :

HET Code:	BB1
Formula:	C16H31N3O4
Molecular weight:	329.435 g/mol
DrugBank ID:	DB04368
Buried Surface Area:	65.21 %
Polar Surface area:	89.95 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-12.6898	-5.571	32.3407

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
O3	N	ILE- 44	2.93	156.15	H-Bond (Protein Donor)	false
C10	CD1	ILE- 44	4.49	0	Hydrophobic	false
C8	CG1	ILE- 44	3.96	0	Hydrophobic	false
O2	NE2	GLN- 50	2.98	149.65	H-Bond (Protein Donor)	false
C10	CG	GLU- 88	4.44	0	Hydrophobic	false
N2	O	GLY- 89	3.29	157.49	H-Bond (Ligand Donor)	false
O4	N	GLY- 89	3.23	128.05	H-Bond (Protein Donor)	false
O2	N	LEU- 91	2.55	163.2	H-Bond (Protein Donor)	false
C14	CD2	LEU- 91	4.41	0	Hydrophobic	false
C13	CD	ARG- 97	4.48	0	Hydrophobic	false
C10	CG2	ILE- 128	3.75	0	Hydrophobic	false
C9	SG	CYS- 129	4.11	0	Hydrophobic	false
C10	CB	CYS- 129	4.19	0	Hydrophobic	false
C9	CB	HIS- 132	3.68	0	Hydrophobic	false
O1	OE1	GLU- 133	2.66	167.98	H-Bond (Protein Donor)	false