scPDB - 2fto entry

Protein Data Bank Entry:

PDB ID : 2fto

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2006-01-24

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
X	100 %

Ligand binding site composition:

B-Factor:	21.753
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	799.875

% Hydrophobic	% Polar
42.19	57.81
According to VolSite

Ligand :

HET Code:	TMP
Formula:	C10H13N2O8P
Molecular weight:	320.193 g/mol
DrugBank ID:	-
Buried Surface Area:	58.04 %
Polar Surface area:	161.1 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
42.6252	-15.0427	41.5343

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
O1P	CZ	ARG- 21	3.61	0	Ionic (Protein Cationic)	false
O1P	NE	ARG- 21	2.75	164.35	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 21	2.87	170.61	H-Bond (Protein Donor)	false
C5M	CH2	TRP- 80	3.68	0	Hydrophobic	false
C5'	CD2	LEU- 143	4.47	0	Hydrophobic	false
C5M	CD2	LEU- 143	4.41	0	Hydrophobic	false
O2P	CZ	ARG- 166	3.62	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 166	3.44	0	Ionic (Protein Cationic)	false
O2P	NH2	ARG- 166	2.84	147.02	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 166	2.69	160.72	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 166	3.33	128.54	H-Bond (Protein Donor)	false
O2P	OG	SER- 167	2.56	171.26	H-Bond (Protein Donor)	false
C2'	CB	SER- 167	4.08	0	Hydrophobic	false
O2	N	ASP- 169	2.89	164.26	H-Bond (Protein Donor)	false
C1'	CB	ASP- 169	3.76	0	Hydrophobic	false
N3	OD1	ASN- 177	2.86	163.12	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 177	2.92	164.19	H-Bond (Protein Donor)	false
O3'	NE2	HIS- 207	2.61	158.92	H-Bond (Protein Donor)	false
O3'	OH	TYR- 209	2.7	157.09	H-Bond (Ligand Donor)	false
O4	O	HOH- 271	3.24	127.58	H-Bond (Protein Donor)	false