scPDB - 2nvk entry

Protein Data Bank Entry:

PDB ID : 2nvk

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2006-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thioredoxin reductase 1, mitochondrial
ID:	TRXR1_DROME
AC:	P91938
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	1.8.1.9

Chains:

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

Ligand binding site composition:

B-Factor:	47.384
Number of residues:	70
Including
Standard Amino Acids:	66
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.363	2244.375

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	72.81 %
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
111.276	25.7925	63.2821

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
C4'	CB	SER- 19	4.35	0	Hydrophobic	false
O4'	OG	SER- 19	3.46	149.14	H-Bond (Protein Donor)	false
O1P	N	ALA- 20	2.86	158.18	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 39	2.88	174.8	H-Bond (Ligand Donor)	false
O2B	O	PHE- 40	2.74	169.58	H-Bond (Ligand Donor)	false
N3A	N	PHE- 40	3.11	148.53	H-Bond (Protein Donor)	false
O1A	OG1	THR- 56	2.67	166.77	H-Bond (Protein Donor)	false
O2A	N	THR- 56	2.91	178.57	H-Bond (Protein Donor)	false
C8M	CG2	THR- 56	3.65	0	Hydrophobic	false
C2'	SG	CYS- 62	4.38	0	Hydrophobic	false
O4	NZ	LYS- 65	2.54	135.38	H-Bond (Protein Donor)	false
N5	NZ	LYS- 65	2.98	137.1	H-Bond (Protein Donor)	false
N6A	O	GLY- 130	2.93	157.57	H-Bond (Ligand Donor)	false
N1A	N	GLY- 130	2.96	172.52	H-Bond (Protein Donor)	false
C7M	CB	SER- 177	3.82	0	Hydrophobic	false
C7M	CE2	PHE- 181	3.89	0	Hydrophobic	false
C7	CG1	ILE- 198	3.67	0	Hydrophobic	false
C8	CD1	ILE- 198	3.78	0	Hydrophobic	false
C8M	CD	ARG- 287	4.16	0	Hydrophobic	false
C2B	CD1	LEU- 290	4.18	0	Hydrophobic	false
O3'	OD2	ASP- 326	3.07	170.71	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 326	4.35	0	Hydrophobic	false
O2P	N	ASP- 326	2.94	159.16	H-Bond (Protein Donor)	false
N1	N	THR- 335	3.45	154.11	H-Bond (Protein Donor)	false
O2	N	THR- 335	3.02	146.98	H-Bond (Protein Donor)	false
C2'	CB	THR- 335	4.45	0	Hydrophobic	false
C4'	CB	THR- 335	4.44	0	Hydrophobic	false
C5'	CB	ALA- 338	4.39	0	Hydrophobic	false
O1P	O	HOH- 492	2.68	178.06	H-Bond (Protein Donor)	false
O2P	O	HOH- 498	2.69	179.96	H-Bond (Protein Donor)	false