scPDB - 3f8r entry

Protein Data Bank Entry:

PDB ID : 3f8r

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2008-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADH oxidase/thioredoxin reductase
ID:	Q8X236_SULSF
AC:	Q8X236
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	2287
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.185
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.413	1373.625

% Hydrophobic	% Polar
49.88	50.12
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	66.21 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
44.7744	85.6699	-26.3938

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
O2N	N	ALA- 26	2.94	164.56	H-Bond (Protein Donor)	false
N3A	N	GLU- 46	3.38	140.01	H-Bond (Protein Donor)	false
O2B	N	THR- 47	3.34	151.97	H-Bond (Protein Donor)	false
O2X	OG1	THR- 47	3.33	132.62	H-Bond (Protein Donor)	false
O3X	OG1	THR- 47	2.62	162.83	H-Bond (Protein Donor)	false
O1A	N	GLN- 51	2.93	163.14	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 51	2.81	156.54	H-Bond (Protein Donor)	false
N6A	O	VAL- 92	3.15	165.16	H-Bond (Ligand Donor)	false
N1A	N	VAL- 92	2.79	173.41	H-Bond (Protein Donor)	false
O1N	N	ASP- 287	2.88	144.49	H-Bond (Protein Donor)	false
O1N	O	HOH- 5059	2.71	179.94	H-Bond (Protein Donor)	false
O2N	O	HOH- 5071	2.59	160.93	H-Bond (Protein Donor)	false