scPDB - 4ivr entry

Protein Data Bank Entry:

PDB ID : 4ivr

Resolution :2.400 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:	39.930
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.051	546.750

% Hydrophobic	% Polar
45.68	54.32
According to VolSite

Ligand :

HET Code:	N50
Formula:	C11H16N2O4
Molecular weight:	240.256 g/mol
DrugBank ID:	-
Buried Surface Area:	73.77 %
Polar Surface area:	84.7 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
20.9791	21.8935	64.1918

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
C14	CZ3	TRP- 88	4.31	0	Hydrophobic	false
C13	CH2	TRP- 88	3.42	0	Hydrophobic	false
C14	CD1	ILE- 97	3.99	0	Hydrophobic	false
C01	CG2	ILE- 100	4.45	0	Hydrophobic	false
C01	CE2	TYR- 101	3.74	0	Hydrophobic	false
C02	CG	GLN- 125	3.46	0	Hydrophobic	false
C02	CB	MET- 128	3.68	0	Hydrophobic	false
C3	CE	MET- 128	3.6	0	Hydrophobic	false
C11	CE	MET- 128	4.27	0	Hydrophobic	false
C4	CE2	TYR- 132	4.18	0	Hydrophobic	false
C4	CD	ARG- 163	3.95	0	Hydrophobic	false
C11	CD	ARG- 163	4.4	0	Hydrophobic	false
C13	CD	ARG- 163	4.31	0	Hydrophobic	false
O3	NH2	ARG- 163	3.43	161.04	H-Bond (Protein Donor)	false
C4	CB	ALA- 167	4.24	0	Hydrophobic	false
C02	CB	ALA- 168	3.64	0	Hydrophobic	false
C4	CB	ALA- 168	4.28	0	Hydrophobic	false
C01	CD2	TYR- 172	4.29	0	Hydrophobic	false
C02	CB	TYR- 172	3.89	0	Hydrophobic	false
C3	CB	TYR- 172	4.29	0	Hydrophobic	false
C4	CD1	TYR- 172	3.97	0	Hydrophobic	false
C11	CZ	TYR- 172	3.8	0	Hydrophobic	false
DuAr	DuAr	TYR- 172	3.73	0	Aromatic Face/Face	false