scPDB - 4gsy entry

Protein Data Bank Entry:

PDB ID : 4gsy

Resolution :1.710 Å

Experimental Method : X-ray

Deposition Date : 2012-08-28

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_STAAR
AC:	Q6GJI9
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	282458
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.231
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.667	381.375

% Hydrophobic	% Polar
63.72	36.28
According to VolSite

Ligand :

HET Code:	0Y5
Formula:	C25H24F3N3O5
Molecular weight:	503.470 g/mol
DrugBank ID:	-
Buried Surface Area:	58.31 %
Polar Surface area:	103.21 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
8.57714	0.252556	27.1717

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
F33	CG	PRO- 38	4.21	0	Hydrophobic	false
F32	CG2	ILE- 47	3.92	0	Hydrophobic	false
O35	CZ	ARG- 48	3.66	0	Ionic (Protein Cationic)	false
O36	CZ	ARG- 48	3.85	0	Ionic (Protein Cationic)	false
O35	NH2	ARG- 48	2.93	142.28	H-Bond (Protein Donor)	false
O36	NE	ARG- 48	3.02	169.71	H-Bond (Protein Donor)	false
C29	CG	ARG- 48	3.91	0	Hydrophobic	false
F33	CB	ARG- 48	3.39	0	Hydrophobic	false
C29	CG1	VAL- 51	4.38	0	Hydrophobic	false
F32	CB	VAL- 51	3.49	0	Hydrophobic	false
C21	CD2	LEU- 52	3.82	0	Hydrophobic	false
C1	CD1	PHE- 66	4.23	0	Hydrophobic	false
F31	CD1	PHE- 66	3.39	0	Hydrophobic	false
F33	CB	SER- 69	3.3	0	Hydrophobic	false
O9	NH2	ARG- 70	2.89	172.4	H-Bond (Protein Donor)	false
C11	CD	ARG- 92	3.81	0	Hydrophobic	false
C1	CB	ARG- 92	3.93	0	Hydrophobic	false
C1	CB	SER- 96	4.1	0	Hydrophobic	false
O9	OG	SER- 97	2.67	153.37	H-Bond (Protein Donor)	false
C12	CE2	TYR- 100	3.7	0	Hydrophobic	false
C11	CZ	TYR- 100	3.78	0	Hydrophobic	false
C10	CD2	TYR- 100	4.04	0	Hydrophobic	false
N7	OE1	GLN- 101	2.79	167.85	H-Bond (Ligand Donor)	false
O6	NE2	GLN- 101	2.83	155.97	H-Bond (Protein Donor)	false