scPDB - 2tps entry

Protein Data Bank Entry:

PDB ID : 2tps

Resolution :1.250 Å

Experimental Method : X-ray

Deposition Date : 1999-03-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiamine-phosphate synthase
ID:	THIE_BACSU
AC:	P39594
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.333
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.527	654.750

% Hydrophobic	% Polar
42.78	57.22
According to VolSite

Ligand :

HET Code:	TPS
Formula:	C12H16N4O4PS
Molecular weight:	343.319 g/mol
DrugBank ID:	DB03416
Buried Surface Area:	69.15 %
Polar Surface area:	166.15 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
63.0603	34.8036	18.9395

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
CM2	CE2	TYR- 29	3.46	0	Hydrophobic	false
CM2	CD1	ILE- 31	3.97	0	Hydrophobic	false
N3A	NE2	GLN- 57	3.04	161.25	H-Bond (Protein Donor)	false
N4A	OE1	GLN- 57	2.93	171.78	H-Bond (Ligand Donor)	false
CM4	CD	ARG- 59	3.65	0	Hydrophobic	false
DuAr	DuAr	HIS- 107	3.76	0	Aromatic Face/Face	false
CM2	CE1	TYR- 147	4.04	0	Hydrophobic	false
O1	OG1	THR- 156	2.74	146.6	H-Bond (Protein Donor)	false
C6	CB	THR- 158	4.45	0	Hydrophobic	false
O2	OG1	THR- 158	2.69	163.23	H-Bond (Protein Donor)	false
S1	CD	LYS- 159	4.17	0	Hydrophobic	false
CM4	CD	LYS- 159	4.37	0	Hydrophobic	false
C6	CB	LYS- 159	3.99	0	Hydrophobic	false
CM2	CG1	VAL- 184	4.06	0	Hydrophobic	false
S1	CG1	ILE- 186	3.95	0	Hydrophobic	false
CM4	CD1	ILE- 186	4.12	0	Hydrophobic	false
C6	CD1	ILE- 186	4.4	0	Hydrophobic	false
C7	CG1	ILE- 186	3.98	0	Hydrophobic	false
C5A	CD1	ILE- 186	3.72	0	Hydrophobic	false
O1	N	GLY- 188	2.95	161.52	H-Bond (Protein Donor)	false
CM4	CD1	ILE- 208	4.17	0	Hydrophobic	false
C6	CD1	ILE- 208	4.05	0	Hydrophobic	false
C7	CG1	ILE- 208	3.83	0	Hydrophobic	false
O3	N	ILE- 208	2.91	172.62	H-Bond (Protein Donor)	false
O2	N	SER- 209	3.09	169.04	H-Bond (Protein Donor)	false
O2	OG	SER- 209	2.8	159.32	H-Bond (Protein Donor)	false
O3	O	HOH- 3003	2.74	179.98	H-Bond (Protein Donor)	false
O3	O	HOH- 3013	2.75	154.64	H-Bond (Protein Donor)	false