scPDB - 4ead entry

Protein Data Bank Entry:

PDB ID : 4ead

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidine phosphorylase
ID:	TYPH_ECOLI
AC:	P07650
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.4.2.4

Chains:

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

Ligand binding site composition:

B-Factor:	21.838
Number of residues:	25
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.186	1080.000

% Hydrophobic	% Polar
44.06	55.94
According to VolSite

Ligand :

HET Code:	0NP
Formula:	C9H11FN5O4
Molecular weight:	272.213 g/mol
DrugBank ID:	-
Buried Surface Area:	65.87 %
Polar Surface area:	129.18 Å2

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

Mass center Coordinates

X	Y	Z
31.3656	-12.2485	-4.14705

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
C1'	CE1	TYR- 168	4.39	0	Hydrophobic	false
O2	NH2	ARG- 171	3.09	147.91	H-Bond (Protein Donor)	false
O2	NH1	ARG- 171	3.15	145.34	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 177	4.32	0	Hydrophobic	false
C4'	CG1	VAL- 177	3.72	0	Hydrophobic	false
F2'	CG2	ILE- 183	3.54	0	Hydrophobic	false
C1'	CG2	ILE- 183	4.44	0	Hydrophobic	false
N3	OG	SER- 186	2.72	160.92	H-Bond (Ligand Donor)	false
F2'	CD1	ILE- 187	3.67	0	Hydrophobic	false
C5'	CD1	PHE- 210	3.62	0	Hydrophobic	false