scPDB - 2x0e entry

Protein Data Bank Entry:

PDB ID : 2x0e

Resolution :2.810 Å

Experimental Method : X-ray

Deposition Date : 2009-12-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	WsaF
ID:	Q7BG50_GEOSE
AC:	Q7BG50
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.093
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.669	1258.875

% Hydrophobic	% Polar
40.21	59.79
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	52.42 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-8.9096	8.96808	-11.6286

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
O2B	N	GLY- 63	2.83	123.67	H-Bond (Protein Donor)	false
C5M	CE1	TYR- 247	3.97	0	Hydrophobic	false
O1B	NH1	ARG- 249	3.13	162.56	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 249	3.05	159.56	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 249	3.76	0	Ionic (Protein Cationic)	false
C5M	CG2	VAL- 282	4.14	0	Hydrophobic	false
O1A	NZ	LYS- 302	2.99	121.56	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 302	2.99	0	Ionic (Protein Cationic)	false
N3	O	LEU- 303	2.68	172.91	H-Bond (Ligand Donor)	false
O4	N	LEU- 303	2.93	128.32	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 305	3.96	0	Hydrophobic	false
C2'	CE2	TYR- 308	4.02	0	Hydrophobic	false
C5M	CE1	TYR- 308	3.63	0	Hydrophobic	false
C3'	CB	TYR- 329	4.3	0	Hydrophobic	false
O3'	OE2	GLU- 333	3.46	131.01	H-Bond (Ligand Donor)	false