scPDB - 1e2k entry

Protein Data Bank Entry:

PDB ID : 1e2k

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2000-05-23

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_HHV11
AC:	P03176
Organism:	Human herpesvirus 1
Reign:	Viruses
TaxID:	10299
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.805
Number of residues:	30
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.499	479.250

% Hydrophobic	% Polar
48.59	51.41
According to VolSite

Ligand :

HET Code:	TMC
Formula:	C12H16N2O4
Molecular weight:	252.266 g/mol
DrugBank ID:	-
Buried Surface Area:	76.58 %
Polar Surface area:	89.87 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
19.989	21.8522	9.32878

Binding mode :

What is Poseview ?

2D View
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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
O18	ND1	HIS- 58	3.48	156.19	H-Bond (Ligand Donor)	false
C10	CB	HIS- 58	3.71	0	Hydrophobic	false
C3	CZ2	TRP- 88	4.06	0	Hydrophobic	false
C12	CZ3	TRP- 88	3.91	0	Hydrophobic	false
C13	CG1	ILE- 97	3.96	0	Hydrophobic	false
C15	CD1	ILE- 97	3.57	0	Hydrophobic	false
C14	CE2	TYR- 101	4.45	0	Hydrophobic	false
O7	NE2	GLN- 125	2.88	170.18	H-Bond (Protein Donor)	false
N5	OE1	GLN- 125	2.89	172.72	H-Bond (Ligand Donor)	false
C13	CE	MET- 128	3.81	0	Hydrophobic	false
C3	CE2	TYR- 132	4.31	0	Hydrophobic	false
O16	NH2	ARG- 163	3.24	142.08	H-Bond (Protein Donor)	false
C3	CD	ARG- 163	3.66	0	Hydrophobic	false
C3	CB	ALA- 167	4.21	0	Hydrophobic	false
C14	CE1	TYR- 172	3.83	0	Hydrophobic	false
C3	CD2	TYR- 172	3.98	0	Hydrophobic	false
C15	CG	GLU- 225	4.45	0	Hydrophobic	false
O9	O	HOH- 2183	2.73	140.06	H-Bond (Protein Donor)	false
O9	O	HOH- 2184	2.78	139.26	H-Bond (Protein Donor)	false