scPDB - 5fuw entry

Protein Data Bank Entry:

PDB ID : 5fuw

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2016-01-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidine kinase, putative
ID:	Q38CF2_TRYB2
AC:	Q38CF2
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	185431
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	57.775
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.514	384.750

% Hydrophobic	% Polar
50.88	49.12
According to VolSite

Ligand :

HET Code:	THM
Formula:	C10H14N2O5
Molecular weight:	242.229 g/mol
DrugBank ID:	DB04485
Buried Surface Area:	73.66 %
Polar Surface area:	99.1 Å2

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

Mass center Coordinates

X	Y	Z
-3.14	-50.5439	-19.8163

Binding mode :

What is Poseview ?

2D View
3D View

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
C5'	CG	MET- 214	3.83	0	Hydrophobic	false
C3'	CE	MET- 214	3.88	0	Hydrophobic	false
C5M	SD	MET- 214	4.41	0	Hydrophobic	false
C2'	SD	MET- 214	3.61	0	Hydrophobic	false
O5'	OE1	GLU- 286	3.02	144.38	H-Bond (Ligand Donor)	false
O5'	OE2	GLU- 286	2.76	150.98	H-Bond (Ligand Donor)	false
C4'	CZ	PHE- 289	3.77	0	Hydrophobic	false
C1'	CZ	PHE- 289	3.78	0	Hydrophobic	false
C5'	CD1	LEU- 312	4.05	0	Hydrophobic	false
C5M	CD1	LEU- 312	3.85	0	Hydrophobic	false
O4	N	TYR- 316	3.05	146.09	H-Bond (Protein Donor)	false
C5M	CB	TYR- 316	4.32	0	Hydrophobic	false
C5M	CG2	THR- 352	3.71	0	Hydrophobic	false
N3	O	ARG- 361	2.93	158.22	H-Bond (Ligand Donor)	false
O2	N	LEU- 363	3.03	172.1	H-Bond (Protein Donor)	false
O3'	N	GLY- 365	3.22	161.14	H-Bond (Protein Donor)	false
C5M	CE1	TYR- 370	3.98	0	Hydrophobic	false
C2'	CE2	TYR- 370	3.4	0	Hydrophobic	false