scPDB - 1e2n entry

Protein Data Bank Entry:

PDB ID : 1e2n

Resolution :2.200 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:	35.802
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.761	411.750

% Hydrophobic	% Polar
46.72	53.28
According to VolSite

Ligand :

HET Code:	RCA
Formula:	C12H16N4O5
Molecular weight:	296.279 g/mol
DrugBank ID:	-
Buried Surface Area:	66.41 %
Polar Surface area:	136.62 Å2

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

Mass center Coordinates

X	Y	Z
19.9329	22.0579	9.02895

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
C12	CB	HIS- 58	3.57	0	Hydrophobic	false
N4	OE2	GLU- 83	2.6	137.95	H-Bond (Ligand Donor)	false
C8	CZ3	TRP- 88	3.35	0	Hydrophobic	false
C8	CD1	ILE- 97	3.79	0	Hydrophobic	false
O3	OH	TYR- 101	3.45	157.93	H-Bond (Protein Donor)	false
O2	NE2	GLN- 125	2.93	164.2	H-Bond (Protein Donor)	false
N2	OE1	GLN- 125	2.74	176.83	H-Bond (Ligand Donor)	false
C8	CE	MET- 128	3.29	0	Hydrophobic	false
C4	CE2	TYR- 132	4.19	0	Hydrophobic	false
C4	CD	ARG- 163	3.81	0	Hydrophobic	false
O5	NE	ARG- 163	3.48	138.76	H-Bond (Protein Donor)	false
O5	NH2	ARG- 163	3.09	154.71	H-Bond (Protein Donor)	false
C4	CB	ALA- 167	4.28	0	Hydrophobic	false
C4	CD1	TYR- 172	3.69	0	Hydrophobic	false
C6	CZ	TYR- 172	3.5	0	Hydrophobic	false
O4	O	HOH- 2081	2.79	179.97	H-Bond (Protein Donor)	false