scPDB - 2qry entry

Protein Data Bank Entry:

PDB ID : 2qry

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2007-07-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiamine-binding periplasmic protein
ID:	THIB_ECOLI
AC:	P31550
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.578
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.074	421.875

% Hydrophobic	% Polar
61.60	38.40
According to VolSite

Ligand :

HET Code:	TPS
Formula:	C12H16N4O4PS
Molecular weight:	343.319 g/mol
DrugBank ID:	DB03416
Buried Surface Area:	81.13 %
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
8.747	50.9551	110.983

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
CM4	CZ	TYR- 27	4.38	0	Hydrophobic	false
C6	CZ	TYR- 27	3.77	0	Hydrophobic	false
C7	CE1	TYR- 27	4.34	0	Hydrophobic	false
O3	OD1	ASP- 59	2.78	145.95	H-Bond (Protein Donor)	false
O2	N	GLY- 60	2.55	131.54	H-Bond (Protein Donor)	false
O1	OG	SER- 161	2.68	136.61	H-Bond (Protein Donor)	false
S1	CG	PRO- 163	4.49	0	Hydrophobic	false
C7	CG	PRO- 163	3.69	0	Hydrophobic	false
CM2	CZ2	TRP- 197	3.96	0	Hydrophobic	false
S1	CB	TRP- 197	3.5	0	Hydrophobic	false
C7	CB	TRP- 197	4.32	0	Hydrophobic	false
S1	CD2	TRP- 197	3.29	0	Hydrophobic	false
O1	N	TRP- 197	3.14	143.55	H-Bond (Protein Donor)	false
CM2	CE1	TYR- 201	4.16	0	Hydrophobic	false
CM4	CZ	TYR- 215	3.77	0	Hydrophobic	false
C6	CZ	TYR- 215	4.43	0	Hydrophobic	false
CM2	CB	SER- 218	4.22	0	Hydrophobic	false
N1A	OG	SER- 218	2.86	143.28	H-Bond (Protein Donor)	false
CM2	CB	TYR- 221	3.52	0	Hydrophobic	false
C5A	CB	TRP- 280	4.09	0	Hydrophobic	false
CM4	SD	MET- 281	3.78	0	Hydrophobic	false
N4A	O	HOH- 438	2.88	143.87	H-Bond (Ligand Donor)	false