scPDB - 2vnk entry

Protein Data Bank Entry:

PDB ID : 2vnk

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2008-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADPH:ferredoxin reductase
ID:	Q9L6V3_RHOCA
AC:	Q9L6V3
Organism:	Rhodobacter capsulatus
Reign:	Bacteria
TaxID:	1061
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.473
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.909	756.000

% Hydrophobic	% Polar
45.54	54.46
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	66.18 %
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
32.0019	28.2951	-4.34898

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
C7M	CE1	PHE- 49	3.93	0	Hydrophobic	false
C2'	CB	ARG- 64	4.07	0	Hydrophobic	false
C3'	CD	ARG- 64	3.93	0	Hydrophobic	false
O1P	NH2	ARG- 64	3.23	132.27	H-Bond (Protein Donor)	false
O1P	NE	ARG- 64	2.89	148.64	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 64	3.47	0	Ionic (Protein Cationic)	false
O2'	O	ALA- 65	2.79	166.83	H-Bond (Ligand Donor)	false
C7	CB	ALA- 65	3.66	0	Hydrophobic	false
C8	CB	ALA- 65	3.71	0	Hydrophobic	false
C8	CB	ALA- 65	3.71	0	Hydrophobic	false
C2'	CE1	TYR- 66	4.28	0	Hydrophobic	false
C4'	CE1	TYR- 66	4.36	0	Hydrophobic	false
O4'	OH	TYR- 66	2.78	135.09	H-Bond (Ligand Donor)	false
O4	N	SER- 67	3.16	140.3	H-Bond (Protein Donor)	false
N3	O	TYR- 80	2.85	168.94	H-Bond (Ligand Donor)	false
O2	N	ILE- 82	2.89	167.12	H-Bond (Protein Donor)	false
C5'	CG2	ILE- 82	4.06	0	Hydrophobic	false
C5'	CG2	VAL- 84	4.37	0	Hydrophobic	false
C5B	CG1	VAL- 84	4.1	0	Hydrophobic	false
O1P	N	LEU- 89	3.03	170.5	H-Bond (Protein Donor)	false
O2P	N	LEU- 89	3.47	121.07	H-Bond (Protein Donor)	false
O2P	OG1	THR- 90	2.7	176.41	H-Bond (Protein Donor)	false
O2P	N	THR- 90	2.86	164.31	H-Bond (Protein Donor)	false
C5'	CG2	THR- 90	3.77	0	Hydrophobic	false
N6A	OG1	THR- 130	2.83	159.17	H-Bond (Ligand Donor)	false
C7M	CG	GLU- 264	4.08	0	Hydrophobic	false
C1'	CB	PHE- 267	3.84	0	Hydrophobic	false
C2B	CD1	PHE- 267	4.05	0	Hydrophobic	false
DuAr	DuAr	PHE- 267	3.79	0	Aromatic Face/Face	false
O2B	O	VAL- 268	3.08	157.67	H-Bond (Ligand Donor)	false
C8M	CG2	VAL- 268	4.19	0	Hydrophobic	false
O2B	N	GLY- 271	3.02	135.11	H-Bond (Protein Donor)	false
C4B	CD1	ILE- 272	3.99	0	Hydrophobic	false
C1B	CG1	ILE- 272	3.72	0	Hydrophobic	false
N3A	N	ILE- 272	3.19	167.52	H-Bond (Protein Donor)	false
O4	O	HOH- 2060	2.92	156.24	H-Bond (Protein Donor)	false