scPDB - 5a65 entry

Protein Data Bank Entry:

PDB ID : 5a65

Resolution :1.980 Å

Experimental Method : X-ray

Deposition Date : 2015-06-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiamine-triphosphatase
ID:	THTPA_MOUSE
AC:	Q8JZL3
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	3.6.1.28

Chains:

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

Ligand binding site composition:

B-Factor:	42.740
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.862	1289.250

% Hydrophobic	% Polar
34.82	65.18
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	49.36 %
Polar Surface area:	225.32 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
37.763	13.9175	4.04565

Binding mode :

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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
O2A	NZ	LYS- 11	2.7	149.95	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 11	2.7	0	Ionic (Protein Cationic)	false
C6	CE2	TYR- 39	4.25	0	Hydrophobic	false
C7	CZ	TYR- 39	4.13	0	Hydrophobic	false
CM4	CE2	TRP- 53	4.4	0	Hydrophobic	false
C6	CB	TRP- 53	4	0	Hydrophobic	false
DuAr	DuAr	TRP- 53	3.72	0	Aromatic Face/Face	false
O3A	NH1	ARG- 55	3.26	146.8	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 55	3.47	127.61	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 55	3.3	131.07	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 55	3.77	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 57	3.58	0	Ionic (Protein Cationic)	false
O3B	NH2	ARG- 57	2.73	152.52	H-Bond (Protein Donor)	false
CM4	CZ	TYR- 79	3.87	0	Hydrophobic	false
CM2	CB	PRO- 191	4.19	0	Hydrophobic	false
S1	CB	ALA- 192	4.09	0	Hydrophobic	false
O1B	NZ	LYS- 193	3.3	128.7	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 193	3.3	0	Ionic (Protein Cationic)	false
S1	CD2	LEU- 194	3.99	0	Hydrophobic	false
CM2	CG	MET- 195	4.14	0	Hydrophobic	false
S1	CE	MET- 195	3.89	0	Hydrophobic	false