scPDB - 1jtq entry

Protein Data Bank Entry:

PDB ID : 1jtq

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2001-08-21

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_ECOLI
AC:	P0A884
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	43.635
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.188	567.000

% Hydrophobic	% Polar
51.79	48.21
According to VolSite

Ligand :

HET Code:	LY3
Formula:	C20H19N9O4
Molecular weight:	449.423 g/mol
DrugBank ID:	DB03038
Buried Surface Area:	56.97 %
Polar Surface area:	205.26 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
47.9851	41.2825	22.1546

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
N7	OG	SER- 54	3.19	151.43	H-Bond (Protein Donor)	false
C14	CB	ILE- 79	3.74	0	Hydrophobic	false
C13	CG2	ILE- 79	3.97	0	Hydrophobic	false
N1	OD2	ASP- 169	3.08	168.65	H-Bond (Ligand Donor)	false
C11	CB	LEU- 172	4.48	0	Hydrophobic	false
N4	O	ALA- 263	2.76	145.03	H-Bond (Ligand Donor)	false
C7	C5	UMP- 565	3.77	0	Hydrophobic	false
N4	O	HOH- 656	3.34	128.8	H-Bond (Ligand Donor)	false
O2	O	HOH- 673	3.23	135.48	H-Bond (Protein Donor)	false