scPDB - 4o7u entry

Protein Data Bank Entry:

PDB ID : 4o7u

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-12-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidylate synthase
ID:	TYSY_ENTFA
AC:	Q834R3
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	8.845
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.105	762.750

% Hydrophobic	% Polar
53.54	46.46
According to VolSite

Ligand :

HET Code:	THF
Formula:	C20H21N7O7
Molecular weight:	471.423 g/mol
DrugBank ID:	DB02800
Buried Surface Area:	52.76 %
Polar Surface area:	224.7 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
13.2261	-18.5437	27.9496

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
CG	CG	PRO- 52	3.98	0	Hydrophobic	false
CG	CD1	LEU- 55	3.96	0	Hydrophobic	false
C15	CD1	ILE- 80	4.2	0	Hydrophobic	false
C11	CG2	ILE- 80	3.96	0	Hydrophobic	false
C12	CB	ILE- 80	3.76	0	Hydrophobic	false
C6	CZ2	TRP- 81	3.65	0	Hydrophobic	false
C9	CE2	TRP- 81	3.78	0	Hydrophobic	false
C9	CZ3	TRP- 84	4.09	0	Hydrophobic	false
N3	OD2	ASP- 220	2.99	138.15	H-Bond (Ligand Donor)	false
CG	CZ	PHE- 227	4.39	0	Hydrophobic	false
NA2	OH	TYR- 260	3.46	122.09	H-Bond (Ligand Donor)	false
C12	CD1	ILE- 313	3.43	0	Hydrophobic	false
NA2	O	ALA- 314	2.99	132.3	H-Bond (Ligand Donor)	false
O1	O	HOH- 506	3.01	156.55	H-Bond (Protein Donor)	false
O3	O	HOH- 562	2.81	144.88	H-Bond (Protein Donor)	false
O4	O	HOH- 567	2.79	179.98	H-Bond (Protein Donor)	false