scPDB - 4ivq entry

Protein Data Bank Entry:

PDB ID : 4ivq

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-01-23

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
A	100 %

Ligand binding site composition:

B-Factor:	32.661
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.375	516.375

% Hydrophobic	% Polar
52.29	47.71
According to VolSite

Ligand :

HET Code:	I43
Formula:	C11H16N2O4
Molecular weight:	240.256 g/mol
DrugBank ID:	-
Buried Surface Area:	71.53 %
Polar Surface area:	82.36 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
20.3368	21.8902	63.7294

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
C13	CB	HIS- 58	3.42	0	Hydrophobic	false
O3	OE2	GLU- 83	3.43	131.83	H-Bond (Ligand Donor)	false
C01	CZ2	TRP- 88	4.48	0	Hydrophobic	false
C14	CZ3	TRP- 88	3.25	0	Hydrophobic	false
C14	CD1	ILE- 97	4.2	0	Hydrophobic	false
C02	CG2	ILE- 100	4.22	0	Hydrophobic	false
C02	CZ	TYR- 101	4.25	0	Hydrophobic	false
C4	CE1	TYR- 101	4.32	0	Hydrophobic	false
O1	NE2	GLN- 125	3.37	140.76	H-Bond (Protein Donor)	false
C01	CE	MET- 128	3.97	0	Hydrophobic	false
C14	CE	MET- 128	4.2	0	Hydrophobic	false
C01	CD	ARG- 163	3.84	0	Hydrophobic	false
O3	NH2	ARG- 163	2.63	156.25	H-Bond (Protein Donor)	false
O3	NE	ARG- 163	3.03	135.76	H-Bond (Protein Donor)	false
C01	CB	ALA- 167	4.5	0	Hydrophobic	false
C01	CD1	TYR- 172	3.99	0	Hydrophobic	false
C02	CD2	TYR- 172	3.37	0	Hydrophobic	false
C4	CE2	TYR- 172	3.62	0	Hydrophobic	false
C02	CE	MET- 231	3.6	0	Hydrophobic	false
O3	O	HOH- 674	2.81	159.03	H-Bond (Ligand Donor)	false