scPDB - 1tvv entry

Protein Data Bank Entry:

PDB ID : 1tvv

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1997-09-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.220	7.610	7.610	0.390	8.000	2

List of CHEMBLId :

CHEMBL389051

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:	32.992
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.139	1221.750

% Hydrophobic	% Polar
47.24	52.76
According to VolSite

Ligand :

HET Code:	CB3
Formula:	C24H21N5O6
Molecular weight:	475.453 g/mol
DrugBank ID:	DB03541
Buried Surface Area:	39.21 %
Polar Surface area:	180.08 Å2

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

Mass center Coordinates

X	Y	Z
19.5589	47.2778	-47.0146

Binding mode :

What is Poseview ?

2D View
3D View

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
CP2	CG2	ILE- 81	4.19	0	Hydrophobic	false
C14	CG2	ILE- 81	3.52	0	Hydrophobic	false
C7	CD2	LEU- 195	4.05	0	Hydrophobic	false
NA2	OD2	ASP- 221	3.29	137.17	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 221	2.94	150.74	H-Bond (Ligand Donor)	false
CP3	CD2	PHE- 228	3.66	0	Hydrophobic	false
CB	CG1	VAL- 314	3.45	0	Hydrophobic	false
C8	C4'	UMP- 317	4.4	0	Hydrophobic	false
C4A	C1'	UMP- 317	3.61	0	Hydrophobic	false