scPDB - 3f8d entry

Protein Data Bank Entry:

PDB ID : 3f8d

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2008-11-12

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
C	3 %
D	97 %

Ligand binding site composition:

B-Factor:	14.809
Number of residues:	62
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.545	1977.750

% Hydrophobic	% Polar
43.17	56.83
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	74.43 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
20.8112	16.7578	22.1737

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
O3B	N	LEU- 23	2.92	142.09	H-Bond (Protein Donor)	false
C4'	CG	PRO- 25	4.07	0	Hydrophobic	false
O1P	N	ALA- 26	2.85	158.16	H-Bond (Protein Donor)	false
N3A	N	GLU- 46	3.17	139.95	H-Bond (Protein Donor)	false
O3B	O	THR- 47	2.7	153.67	H-Bond (Ligand Donor)	false
C2B	CB	THR- 47	4.42	0	Hydrophobic	false
O2B	N	THR- 47	2.98	141.03	H-Bond (Protein Donor)	false
O1A	NE2	GLN- 51	2.96	160.19	H-Bond (Protein Donor)	false
O2A	N	GLN- 51	2.85	164.51	H-Bond (Protein Donor)	false
C8M	CB	GLN- 51	3.95	0	Hydrophobic	false
C7M	CB	GLU- 54	4.02	0	Hydrophobic	false
C6	CB	ALA- 55	3.53	0	Hydrophobic	false
N3	OD1	ASP- 60	2.72	154.82	H-Bond (Ligand Donor)	false
N6A	O	VAL- 92	2.99	171.6	H-Bond (Ligand Donor)	false
N1A	N	VAL- 92	2.83	172.22	H-Bond (Protein Donor)	false
C8M	CD	ARG- 125	4.32	0	Hydrophobic	false
C7M	CB	TYR- 143	3.59	0	Hydrophobic	false
C6	CB	CYS- 144	3.95	0	Hydrophobic	false
C9A	SG	CYS- 144	4.26	0	Hydrophobic	false
C8M	CE2	PHE- 249	4.3	0	Hydrophobic	false
O3'	OD2	ASP- 287	3.13	153.32	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 287	3.03	140.32	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 287	4.06	0	Hydrophobic	false
O2P	N	ASP- 287	2.87	152.91	H-Bond (Protein Donor)	false
N1	N	VAL- 298	3.45	132.01	H-Bond (Protein Donor)	false
O2	N	VAL- 298	2.69	168.87	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 298	4.04	0	Hydrophobic	false
C5'	CB	ALA- 301	4.2	0	Hydrophobic	false
O2P	O	HOH- 5003	2.66	159.14	H-Bond (Protein Donor)	false
O1P	O	HOH- 5063	2.73	179.98	H-Bond (Protein Donor)	false