scPDB - 1lce entry

Protein Data Bank Entry:

PDB ID : 1lce

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1995-06-22

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_LACCA
AC:	P00469
Organism:	Lactobacillus casei
Reign:	Bacteria
TaxID:	1582
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.873
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.078	958.500

% Hydrophobic	% Polar
41.20	58.80
According to VolSite

Ligand :

HET Code:	TMF
Formula:	C20H19N7O6
Molecular weight:	453.408 g/mol
DrugBank ID:	DB02301
Buried Surface Area:	58.54 %
Polar Surface area:	195.67 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.6095	47.0612	-46.6412

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
O2	NZ	LYS- 50	3.02	167.49	H-Bond (Protein Donor)	false
O2	NZ	LYS- 50	3.02	0	Ionic (Protein Cationic)	false
C13	CD1	ILE- 81	3.91	0	Hydrophobic	false
C15	CG2	ILE- 81	3.68	0	Hydrophobic	false
C9	CG2	ILE- 81	3.3	0	Hydrophobic	false
C6	CZ2	TRP- 82	3.27	0	Hydrophobic	false
N3	OH	TYR- 146	3.44	162.07	H-Bond (Protein Donor)	false
NA2	O	PRO- 196	3.22	123.82	H-Bond (Ligand Donor)	false
CB	CD2	LEU- 224	3.41	0	Hydrophobic	false
O1	N	GLY- 225	2.52	129.35	H-Bond (Protein Donor)	false
CB	CE1	PHE- 228	4.33	0	Hydrophobic	false
C12	CG	PHE- 228	3.39	0	Hydrophobic	false