scPDB - 3uwo entry

Protein Data Bank Entry:

PDB ID : 3uwo

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidylate kinase
ID:	KTHY_PSEAE
AC:	Q9HZN8
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	2.7.4.9

Chains:

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

Ligand binding site composition:

B-Factor:	27.473
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.638	587.250

% Hydrophobic	% Polar
57.47	42.53
According to VolSite

Ligand :

HET Code:	0DJ
Formula:	C14H12N4O2
Molecular weight:	268.271 g/mol
DrugBank ID:	-
Buried Surface Area:	82 %
Polar Surface area:	88.32 Å2

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

Mass center Coordinates

X	Y	Z
8.5564	-1.17895	6.0985

Binding mode :

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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
C10	CB	GLU- 39	3.59	0	Hydrophobic	false
C14	CD2	LEU- 54	4.1	0	Hydrophobic	false
C10	SD	MET- 70	4.05	0	Hydrophobic	false
C4	CE	MET- 70	3.58	0	Hydrophobic	false
O11	NH2	ARG- 74	2.88	164.92	H-Bond (Protein Donor)	false
C10	CB	ARG- 96	3.92	0	Hydrophobic	false
C3	CD	ARG- 96	3.45	0	Hydrophobic	false
C2	CD	ARG- 96	4.09	0	Hydrophobic	false
DuAr	CZ	ARG- 96	3.89	8.56	Pi/Cation	false
C10	CB	ALA- 100	4.03	0	Hydrophobic	false
C4	CB	ALA- 100	3.77	0	Hydrophobic	false
O11	OG1	THR- 101	2.58	134.25	H-Bond (Protein Donor)	false
O19	OH	TYR- 104	2.55	142.66	H-Bond (Protein Donor)	false
N6	NE2	GLN- 105	3.27	169.27	H-Bond (Protein Donor)	false
N9	OE1	GLN- 105	2.77	165.15	H-Bond (Ligand Donor)	false
C17	CB	PHE- 155	3.87	0	Hydrophobic	false