scPDB - 4ez8 entry

Protein Data Bank Entry:

PDB ID : 4ez8

Resolution :1.170 Å

Experimental Method : X-ray

Deposition Date : 2012-05-02

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_MOUSE
AC:	P07607
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.1.1.45

Chains:

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

Ligand binding site composition:

B-Factor:	11.675
Number of residues:	43
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.150	826.875

% Hydrophobic	% Polar
45.31	54.69
According to VolSite

Ligand :

HET Code:	DHF
Formula:	C19H19N7O6
Molecular weight:	441.397 g/mol
DrugBank ID:	DB02015
Buried Surface Area:	54.57 %
Polar Surface area:	213.26 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
22.851	-19.8701	8.70909

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	CD2	PHE- 74	3.93	0	Hydrophobic	false
C11	CG2	ILE- 102	3.6	0	Hydrophobic	false
C15	CB	ILE- 102	3.63	0	Hydrophobic	false
C9	CZ2	TRP- 103	3.51	0	Hydrophobic	false
NA2	OD2	ASP- 212	3.45	129.33	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 212	2.72	167.28	H-Bond (Ligand Donor)	false
C11	CD1	LEU- 215	3.99	0	Hydrophobic	false
C16	CD2	LEU- 215	4.2	0	Hydrophobic	false
C16	SD	MET- 305	4.22	0	Hydrophobic	false
NA2	O	ALA- 306	2.91	147.38	H-Bond (Ligand Donor)	false
NA2	O	HOH- 509	3.4	128.3	H-Bond (Ligand Donor)	false
O2	O	HOH- 515	3	150.39	H-Bond (Protein Donor)	false
OE1	O	HOH- 540	2.69	179.95	H-Bond (Protein Donor)	false
O1	O	HOH- 559	2.68	153.82	H-Bond (Protein Donor)	false
N1	O	HOH- 609	2.87	158.85	H-Bond (Protein Donor)	false