scPDB - 5fsi entry

Protein Data Bank Entry:

PDB ID : 5fsi

Resolution :1.630 Å

Experimental Method : X-ray

Deposition Date : 2016-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	7,8-dihydro-8-oxoguanine triphosphatase
ID:	8ODP_HUMAN
AC:	P36639
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.6.1.55

Chains:

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

Ligand binding site composition:

B-Factor:	17.505
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.599	364.500

% Hydrophobic	% Polar
48.15	51.85
According to VolSite

Ligand :

HET Code:	8DG
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	-
Buried Surface Area:	59.84 %
Polar Surface area:	329.85 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
10.6738	21.7369	2.78741

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
C5'	CD2	TYR- 7	3.88	0	Hydrophobic	false
C3'	CD2	TYR- 7	4.14	0	Hydrophobic	false
C2'	CB	TYR- 7	4.26	0	Hydrophobic	false
O3'	O	THR- 8	2.75	148.9	H-Bond (Ligand Donor)	false
C1'	CD1	LEU- 9	4.22	0	Hydrophobic	false
C5'	CD2	PHE- 27	4.41	0	Hydrophobic	false
N2	OD1	ASN- 33	2.77	134.87	H-Bond (Ligand Donor)	false
N3	ND2	ASN- 33	2.82	156.85	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 38	3.02	143.73	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 38	3.31	124.02	H-Bond (Protein Donor)	false
O1B	N	LYS- 38	2.85	170.19	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 38	3.02	0	Ionic (Protein Cationic)	false
C5'	CE	MET- 81	4.44	0	Hydrophobic	false
C2'	CG1	VAL- 83	4.08	0	Hydrophobic	false
O6	OD2	ASP- 119	3.29	124.63	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 119	3.33	123.18	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 120	3.05	147.49	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 120	2.98	132.56	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 120	2.92	153.5	H-Bond (Ligand Donor)	false
O4'	O	HOH- 2008	2.9	179.96	H-Bond (Protein Donor)	false