scPDB - 4iji entry

Protein Data Bank Entry:

PDB ID : 4iji

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-12-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutathione S-transferase-like protein YibF
ID:	Q4K4R5_PSEF5
AC:	Q4K4R5
Organism:	Pseudomonas fluorescens
Reign:	Bacteria
TaxID:	220664
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
E	16 %
G	84 %

Ligand binding site composition:

B-Factor:	14.393
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.448	1933.875

% Hydrophobic	% Polar
40.66	59.34
According to VolSite

Ligand :

HET Code:	99T
Formula:	C13H19N3O8S
Molecular weight:	377.370 g/mol
DrugBank ID:	-
Buried Surface Area:	66.92 %
Polar Surface area:	231.53 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
31.909	-28.4392	48.7249

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
C08	CB	SER- 9	3.78	0	Hydrophobic	false
SG2	CB	SER- 9	3.51	0	Hydrophobic	false
SG2	CD2	TYR- 11	3.8	0	Hydrophobic	false
CG1	CD2	TYR- 11	3.3	0	Hydrophobic	false
CB1	CE1	TYR- 11	3.82	0	Hydrophobic	false
CG1	CD	LYS- 52	4.18	0	Hydrophobic	false
O2	N	ILE- 53	2.9	162.05	H-Bond (Protein Donor)	false
CB2	CG1	ILE- 53	4.34	0	Hydrophobic	false
N2	O	ILE- 53	2.92	150.1	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 66	2.83	147.91	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 66	2.83	0	Ionic (Ligand Cationic)	false
O01	OG	SER- 67	2.53	167.5	H-Bond (Protein Donor)	false
O02	N	SER- 67	2.9	147.28	H-Bond (Protein Donor)	false
O02	OG	SER- 67	3.33	132.32	H-Bond (Protein Donor)	false
SG2	CG2	VAL- 109	4.21	0	Hydrophobic	false
C09	CG2	VAL- 109	4.47	0	Hydrophobic	false
N3	OH	TYR- 113	2.8	130.75	H-Bond (Ligand Donor)	false
C09	CZ	TYR- 113	4.4	0	Hydrophobic	false
O32	NZ	LYS- 134	2.62	150.94	H-Bond (Protein Donor)	false
O32	NZ	LYS- 134	2.62	0	Ionic (Protein Cationic)	false
O31	NZ	LYS- 134	3.55	0	Ionic (Protein Cationic)	false
C08	CE1	TYR- 167	4.23	0	Hydrophobic	false
C09	CZ	TYR- 167	4.25	0	Hydrophobic	false
O12	OH	TYR- 167	2.52	170.85	H-Bond (Protein Donor)	false
O11	NH2	ARG- 171	3.27	169.27	H-Bond (Protein Donor)	false
O12	NH2	ARG- 171	3.42	136.2	H-Bond (Protein Donor)	false
O12	NE	ARG- 171	2.95	166.7	H-Bond (Protein Donor)	false
O12	CZ	ARG- 171	3.63	0	Ionic (Protein Cationic)	false