scPDB - 2f17 entry

Protein Data Bank Entry:

PDB ID : 2f17

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2005-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiamin pyrophosphokinase 1
ID:	TPK1_MOUSE
AC:	Q9R0M5
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.7.6.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	43 %
B	57 %

Ligand binding site composition:

B-Factor:	44.048
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.205	533.250

% Hydrophobic	% Polar
30.38	69.62
According to VolSite

Ligand :

HET Code:	PYI
Formula:	C14H18N4O7P2
Molecular weight:	416.263 g/mol
DrugBank ID:	DB04768
Buried Surface Area:	58.84 %
Polar Surface area:	197.08 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
6.52219	69.9511	17.1021

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	CB	GLN- 96	4.42	0	Hydrophobic	false
N4A	O	GLN- 96	2.95	145.17	H-Bond (Ligand Donor)	false
N4A	OD1	ASP- 97	2.94	140.91	H-Bond (Ligand Donor)	false
C6	CG2	THR- 99	3.74	0	Hydrophobic	false
O1B	NH1	ARG- 131	3.27	128.2	H-Bond (Protein Donor)	false
CM2	CB	TRP- 202	4.08	0	Hydrophobic	false
C5A	CB	TRP- 202	4.12	0	Hydrophobic	false
CM4	CH2	TRP- 202	3.65	0	Hydrophobic	false
CM2	CD1	LEU- 204	3.96	0	Hydrophobic	false
CM2	CD1	LEU- 214	4.27	0	Hydrophobic	false
CM2	CB	SER- 216	4.11	0	Hydrophobic	false
N1A	OG	SER- 216	2.87	164.82	H-Bond (Protein Donor)	false
C5	CB	SER- 218	4.08	0	Hydrophobic	false
CM7	CB	SER- 218	3.78	0	Hydrophobic	false
CM4	CB	SER- 218	3.93	0	Hydrophobic	false
O2A	MG	MG- 902	2.45	0	Metal Acceptor	false
O2B	MG	MG- 902	2.45	0	Metal Acceptor	false
O3B	O	HOH- 2234	3.29	179.98	H-Bond (Protein Donor)	false