scPDB - 1p6x entry

Protein Data Bank Entry:

PDB ID : 1p6x

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2003-04-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidine kinase
ID:	KITH_EHV4
AC:	P24425
Organism:	Equine herpesvirus 4
Reign:	Viruses
TaxID:	10333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.081
Number of residues:	28
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.803	502.875

% Hydrophobic	% Polar
50.34	49.66
According to VolSite

Ligand :

HET Code:	THM
Formula:	C10H14N2O5
Molecular weight:	242.229 g/mol
DrugBank ID:	DB04485
Buried Surface Area:	73.54 %
Polar Surface area:	99.1 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
23.2883	18.8166	43.2621

Binding mode :

What is Poseview ?

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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
C3'	CG	TYR- 34	3.78	0	Hydrophobic	false
C2'	CD2	TYR- 34	3.52	0	Hydrophobic	false
O5'	OE2	GLU- 60	2.94	158.84	H-Bond (Ligand Donor)	false
C5'	CE	MET- 62	4.34	0	Hydrophobic	false
C5'	CZ3	TRP- 65	3.87	0	Hydrophobic	false
C5M	CH2	TRP- 65	3.79	0	Hydrophobic	false
C5'	CD1	ILE- 74	4.22	0	Hydrophobic	false
C4'	CG1	ILE- 74	3.92	0	Hydrophobic	false
O3'	OH	TYR- 78	2.93	157.43	H-Bond (Protein Donor)	false
N3	OE1	GLN- 102	3.01	176.84	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 102	2.71	163.83	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 105	3.75	0	Hydrophobic	false
C5M	CD2	PHE- 105	4.34	0	Hydrophobic	false
C5M	CD	ARG- 139	3.62	0	Hydrophobic	false
C5M	CB	ALA- 143	4.46	0	Hydrophobic	false
C5M	CB	SER- 144	4.3	0	Hydrophobic	false
C5M	CE1	PHE- 148	4.19	0	Hydrophobic	false
C2'	CE2	PHE- 148	3.62	0	Hydrophobic	false
O2	O	HOH- 824	2.59	163.76	H-Bond (Protein Donor)	false
O2	O	HOH- 825	3.03	144.41	H-Bond (Protein Donor)	false