scPDB - 1p7c entry

Protein Data Bank Entry:

PDB ID : 1p7c

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2003-05-01

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:	27.326
Number of residues:	49
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.739	874.125

% Hydrophobic	% Polar
49.42	50.58
According to VolSite

Ligand :

HET Code:	T5A
Formula:	C20H25N7O23P5
Molecular weight:	886.314 g/mol
DrugBank ID:	DB03280
Buried Surface Area:	69.35 %
Polar Surface area:	503.26 Å2

Number of
H-Bond Acceptors:	27
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
54.5677	79.9705	54.7353

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
C3E	CB	HIS- 58	3.97	0	Hydrophobic	false
O2C	N	GLY- 59	3.3	155.3	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 62	3.63	0	Ionic (Protein Cationic)	false
O1C	NZ	LYS- 62	2.78	0	Ionic (Protein Cationic)	false
O2C	NZ	LYS- 62	3.8	0	Ionic (Protein Cationic)	false
O1C	NZ	LYS- 62	2.78	172.79	H-Bond (Protein Donor)	false
O1D	N	LYS- 62	2.92	129.33	H-Bond (Protein Donor)	false
O1C	OG1	THR- 63	3.32	128.83	H-Bond (Protein Donor)	false
O2E	OG1	THR- 64	2.51	162	H-Bond (Protein Donor)	false
O2E	N	THR- 64	2.99	152.32	H-Bond (Protein Donor)	false
C4E	CD1	ILE- 97	3.66	0	Hydrophobic	false
O3E	OH	TYR- 101	2.79	146.79	H-Bond (Protein Donor)	false
N3B	OE1	GLN- 125	2.87	172.14	H-Bond (Ligand Donor)	false
O4B	NE2	GLN- 125	2.78	165.41	H-Bond (Protein Donor)	false
C7B	CE	MET- 128	4.48	0	Hydrophobic	false
C1E	CE	MET- 128	4.18	0	Hydrophobic	false
C7B	CE2	TYR- 132	4.16	0	Hydrophobic	false
C7B	CD	ARG- 163	3.58	0	Hydrophobic	false
O2A	NE	ARG- 163	2.71	144.63	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 163	2.73	140.51	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 163	3.13	0	Ionic (Protein Cationic)	false
C7B	CD1	TYR- 172	4.39	0	Hydrophobic	false
C2E	CE2	TYR- 172	3.79	0	Hydrophobic	false
C1F	CG	ARG- 216	4.19	0	Hydrophobic	false
C4F	CG	ARG- 216	4.05	0	Hydrophobic	false
DuAr	CZ	ARG- 216	3.54	159.61	Pi/Cation	false
C4F	CB	LYS- 219	4.45	0	Hydrophobic	false
C1F	CD	LYS- 219	4.21	0	Hydrophobic	false
N3A	NZ	LYS- 219	3	152.68	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 220	3.99	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 220	2.81	135.59	H-Bond (Protein Donor)	false
O1E	NE	ARG- 220	3.1	145.61	H-Bond (Protein Donor)	false
C3F	CG	ARG- 220	4.11	0	Hydrophobic	false
O2D	NH2	ARG- 222	3.08	149.06	H-Bond (Protein Donor)	false
O2D	NH1	ARG- 222	3.09	148.39	H-Bond (Protein Donor)	false
O2D	CZ	ARG- 222	3.53	0	Ionic (Protein Cationic)	false
O3E	OE1	GLU- 225	3.35	133.46	H-Bond (Ligand Donor)	false
N6A	O	GLN- 331	2.91	169.93	H-Bond (Ligand Donor)	false
O2B	O	HOH- 593	2.8	179.98	H-Bond (Protein Donor)	false
O2B	O	HOH- 608	3.05	179.97	H-Bond (Protein Donor)	false
O2C	O	HOH- 637	2.69	179.97	H-Bond (Protein Donor)	false