scPDB - 4oxi entry

Protein Data Bank Entry:

PDB ID : 4oxi

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2014-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Enterobactin synthetase component F-related protein
ID:	Q9KRQ7_VIBCH
AC:	Q9KRQ7
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.878
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.140	823.500

% Hydrophobic	% Polar
43.85	56.15
According to VolSite

Ligand :

HET Code:	GAP
Formula:	C12H17N6O8P
Molecular weight:	404.273 g/mol
DrugBank ID:	-
Buried Surface Area:	78.19 %
Polar Surface area:	232.41 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
34.2162	18.3555	2.36385

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
N	OD2	ASP- 247	3.27	121.99	H-Bond (Ligand Donor)	false
N	OD1	ASP- 247	2.73	163.61	H-Bond (Ligand Donor)	false
N	OD2	ASP- 247	3.27	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 247	2.73	0	Ionic (Ligand Cationic)	false
N7	N	GLY- 317	2.96	138.93	H-Bond (Protein Donor)	false
N6	OD1	ASN- 338	2.94	133.39	H-Bond (Ligand Donor)	false
N6	O	LEU- 339	2.72	158.67	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 340	3.81	0	Hydrophobic	false
C5'	CB	PRO- 342	3.99	0	Hydrophobic	false
O1A	N	THR- 343	3.05	159.36	H-Bond (Protein Donor)	false
O1A	OG1	THR- 343	2.97	153.78	H-Bond (Protein Donor)	false
N	O	ILE- 347	2.68	159.59	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 432	2.62	156.06	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 432	3.28	142.26	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 432	2.58	168.35	H-Bond (Ligand Donor)	false
O2A	NZ	LYS- 452	3.46	0	Ionic (Protein Cationic)	false
O5'	NZ	LYS- 452	2.85	146.56	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 457	3.74	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 457	2.64	151.39	H-Bond (Protein Donor)	false
N1	O	HOH- 800	2.91	179.97	H-Bond (Protein Donor)	false