scPDB - 2tsr entry

Protein Data Bank Entry:

PDB ID : 2tsr

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 1998-06-19

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_RAT
AC:	P45352
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.1.1.45

Chains:

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

Ligand binding site composition:

B-Factor:	40.423
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.744	675.000

% Hydrophobic	% Polar
52.50	47.50
According to VolSite

Ligand :

HET Code:	D16
Formula:	C21H20N4O6S
Molecular weight:	456.472 g/mol
DrugBank ID:	DB00293
Buried Surface Area:	43.75 %
Polar Surface area:	182.3 Å2

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

Mass center Coordinates

X	Y	Z
4.73119	14.9013	25.7833

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
CB	CD2	PHE- 74	4.3	0	Hydrophobic	false
OE1	N	ARG- 101	2.97	120.53	H-Bond (Protein Donor)	false
S13	CG2	ILE- 102	3.92	0	Hydrophobic	false
C9	CH2	TRP- 103	3.6	0	Hydrophobic	false
N3	OD2	ASP- 212	2.9	129.53	H-Bond (Ligand Donor)	false
S13	CD2	LEU- 215	4.15	0	Hydrophobic	false
C4A	CD2	LEU- 215	4.15	0	Hydrophobic	false
O4	N	GLY- 216	3.04	125.57	H-Bond (Protein Donor)	false
CP1	CD2	PHE- 219	3.79	0	Hydrophobic	false
CM2	CE1	TYR- 252	3.61	0	Hydrophobic	false
C4A	C1'	UMP- 408	3.7	0	Hydrophobic	false