scPDB - 1f4e entry

Protein Data Bank Entry:

PDB ID : 1f4e

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2000-06-07

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	100 %

Ligand binding site composition:

B-Factor:	31.769
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.885	982.125

% Hydrophobic	% Polar
36.08	63.92
According to VolSite

Ligand :

HET Code:	TPR
Formula:	C12H14NO4S
Molecular weight:	268.309 g/mol
DrugBank ID:	DB02752
Buried Surface Area:	50.87 %
Polar Surface area:	85.89 Å2

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

Mass center Coordinates

X	Y	Z
36.1379	59.5457	81.2474

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
C1	CD1	ILE- 55	3.43	0	Hydrophobic	false
C1	CD1	ILE- 79	4.32	0	Hydrophobic	false
CD	CD1	ILE- 79	4.17	0	Hydrophobic	false
C7	CG2	ILE- 79	4.05	0	Hydrophobic	false
CG	CE2	TRP- 80	3.79	0	Hydrophobic	false
CB	CZ2	TRP- 80	3.49	0	Hydrophobic	false
O	OH	TYR- 94	3.45	165.17	H-Bond (Protein Donor)	false
OXT	NE2	HIS- 147	3.3	123.37	H-Bond (Protein Donor)	false
C3	CD1	LEU- 172	4.45	0	Hydrophobic	false
C7	CE2	PHE- 176	3.49	0	Hydrophobic	false
C1	CB	PHE- 176	3.68	0	Hydrophobic	false
O9	ND2	ASN- 177	2.87	128.16	H-Bond (Protein Donor)	false