scPDB - 2uz3 entry

Protein Data Bank Entry:

PDB ID : 2uz3

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-04-24

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_UREPA
AC:	Q9PPP5
Organism:	Ureaplasma parvum serovar 3
Reign:	Bacteria
TaxID:	273119
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	5 %
D	95 %

Ligand binding site composition:

B-Factor:	45.909
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.137	813.375

% Hydrophobic	% Polar
36.93	63.07
According to VolSite

Ligand :

HET Code:	TTP
Formula:	C10H13N2O14P3
Molecular weight:	478.137 g/mol
DrugBank ID:	DB02452
Buried Surface Area:	73.14 %
Polar Surface area:	279.44 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
13.6172	54.2581	47.269

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
C5M	SD	MET- 21	4.03	0	Hydrophobic	false
C3'	CE	MET- 21	3.63	0	Hydrophobic	false
O2B	N	PHE- 22	2.89	158.17	H-Bond (Protein Donor)	false
O2G	N	ALA- 23	3.38	131.29	H-Bond (Protein Donor)	false
O2G	N	GLY- 24	2.91	121.2	H-Bond (Protein Donor)	false
O3G	N	GLY- 24	3.41	136.28	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 25	2.72	167.86	H-Bond (Protein Donor)	false
O2G	N	LYS- 25	2.68	164.63	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 25	2.9	172.46	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 25	2.72	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 25	3.92	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 25	2.9	0	Ionic (Protein Cationic)	false
O1G	N	THR- 26	2.98	162.39	H-Bond (Protein Donor)	false
C4'	CZ	PHE- 100	4.22	0	Hydrophobic	false
C1'	CZ	PHE- 100	3.92	0	Hydrophobic	false
C5'	CD1	LEU- 124	3.94	0	Hydrophobic	false
C5M	CD1	LEU- 124	3.84	0	Hydrophobic	false
O4	N	PHE- 128	2.8	137.9	H-Bond (Protein Donor)	false
C5M	CE2	PHE- 133	4.39	0	Hydrophobic	false
C5M	CB	SER- 163	3.52	0	Hydrophobic	false
N3	O	ILE- 178	2.76	162.17	H-Bond (Ligand Donor)	false
O2	N	LYS- 180	2.79	167.6	H-Bond (Protein Donor)	false
O3'	N	GLY- 182	3.38	167.63	H-Bond (Protein Donor)	false
C5M	CE2	TYR- 187	3.76	0	Hydrophobic	false
C2'	CE1	TYR- 187	3.58	0	Hydrophobic	false
O1A	MG	MG- 4219	1.98	0	Metal Acceptor	false
O1G	MG	MG- 4219	2.55	0	Metal Acceptor	false