scPDB - 1ddu entry

Protein Data Bank Entry:

PDB ID : 1ddu

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1997-06-26

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	7 %
B	93 %

Ligand binding site composition:

B-Factor:	25.401
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.877	918.000

% Hydrophobic	% Polar
39.71	60.29
According to VolSite

Ligand :

HET Code:	DDU
Formula:	C9H12N2O4
Molecular weight:	212.203 g/mol
DrugBank ID:	DB03274
Buried Surface Area:	51.15 %
Polar Surface area:	78.87 Å2

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

Mass center Coordinates

X	Y	Z
44.9225	33.8233	24.7469

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
C5'	SG	CYS- 146	3.98	0	Hydrophobic	false
C2'	SG	CYS- 146	3.57	0	Hydrophobic	false
C2'	CB	SER- 167	3.93	0	Hydrophobic	false
O2	N	ASP- 169	2.82	170.77	H-Bond (Protein Donor)	false
C1'	CB	ASP- 169	4.3	0	Hydrophobic	false
N3	OD1	ASN- 177	3.31	151.09	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 177	3.09	150.67	H-Bond (Protein Donor)	false
O3'	NE2	HIS- 207	2.83	166.35	H-Bond (Ligand Donor)	false
O3'	OH	TYR- 209	2.86	155.8	H-Bond (Protein Donor)	false