scPDB - 1tdu entry

Protein Data Bank Entry:

PDB ID : 1tdu

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1997-06-25

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	97 %
B	3 %

Ligand binding site composition:

B-Factor:	24.035
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.986	918.000

% Hydrophobic	% Polar
44.12	55.88
According to VolSite

Ligand :

HET Code:	CB3
Formula:	C24H21N5O6
Molecular weight:	475.453 g/mol
DrugBank ID:	DB03541
Buried Surface Area:	57.58 %
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
14.6516	14.5609	35.07

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
OE2	NZ	LYS- 48	4	0	Ionic (Protein Cationic)	false
OE1	N	HIS- 51	2.95	161.03	H-Bond (Protein Donor)	false
CP1	CD1	ILE- 79	4.16	0	Hydrophobic	false
C11	CG2	ILE- 79	4.11	0	Hydrophobic	false
C13	CB	ILE- 79	3.59	0	Hydrophobic	false
C9	CZ2	TRP- 80	3.7	0	Hydrophobic	false
CP1	CZ2	TRP- 80	4.39	0	Hydrophobic	false
C8	CZ2	TRP- 83	3.26	0	Hydrophobic	false
C8	CD2	LEU- 143	4.18	0	Hydrophobic	false
NA2	OD2	ASP- 169	3.4	132.44	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 169	2.78	168.34	H-Bond (Ligand Donor)	false
C15	CB	PHE- 176	4.23	0	Hydrophobic	false
CP1	CD2	PHE- 176	4.09	0	Hydrophobic	false
CP3	CB	PHE- 176	3.64	0	Hydrophobic	false
O1	NZ	LYS- 259	3.45	125.86	H-Bond (Protein Donor)	false
O1	NZ	LYS- 259	3.45	0	Ionic (Protein Cationic)	false
NA2	O	ALA- 263	3.43	139.83	H-Bond (Ligand Donor)	false
NA2	O	HOH- 769	2.84	133.79	H-Bond (Ligand Donor)	false