scPDB - 1syn entry

Protein Data Bank Entry:

PDB ID : 1syn

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1995-09-19

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_ECOLI
AC:	P0A884
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.017
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.210	604.125

% Hydrophobic	% Polar
56.98	43.02
According to VolSite

Ligand :

HET Code:	F89
Formula:	C27H22N4O6
Molecular weight:	498.487 g/mol
DrugBank ID:	-
Buried Surface Area:	57.24 %
Polar Surface area:	154.06 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
46.7441	40.8886	21.3567

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
O1	NE2	HIS- 51	3.07	140.38	H-Bond (Protein Donor)	false
O2	NE2	HIS- 51	3.07	160.64	H-Bond (Protein Donor)	false
O	OG	SER- 54	3.14	168.98	H-Bond (Protein Donor)	false
C17	CB	SER- 54	3.46	0	Hydrophobic	false
N12	OE1	GLU- 58	3.27	170.4	H-Bond (Ligand Donor)	false
OE2	OG1	THR- 78	2.72	160.69	H-Bond (Protein Donor)	false
C13	CG2	ILE- 79	4.32	0	Hydrophobic	false
C14	CG1	ILE- 79	3.99	0	Hydrophobic	false
C15	CB	ILE- 79	4.19	0	Hydrophobic	false
CG	CB	ILE- 79	3.97	0	Hydrophobic	false
C1B	CG1	ILE- 79	4.21	0	Hydrophobic	false
C7	CG1	ILE- 79	3.79	0	Hydrophobic	false
OE2	N	ILE- 79	3.06	135.81	H-Bond (Protein Donor)	false
C7	CZ2	TRP- 80	3.49	0	Hydrophobic	false
C5	CD2	LEU- 143	3.8	0	Hydrophobic	false
N2	OD2	ASP- 169	2.96	153.36	H-Bond (Ligand Donor)	false
C11	CB	PHE- 176	3.98	0	Hydrophobic	false
C13	CB	PHE- 176	3.92	0	Hydrophobic	false
DuAr	DuAr	PHE- 176	3.7	0	Aromatic Face/Face	false
C3M	CE2	TYR- 209	4.05	0	Hydrophobic	false
C3M	CG2	VAL- 262	4.09	0	Hydrophobic	false
C3M	CB	ALA- 263	4.16	0	Hydrophobic	false
C3M	C4'	UMP- 300	4.15	0	Hydrophobic	false
C1A	C1'	UMP- 300	4.07	0	Hydrophobic	false