scPDB - 1vfr entry

Protein Data Bank Entry:

PDB ID : 1vfr

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1998-01-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Major NAD(P)H-flavin oxidoreductase
ID:	FRA1_ALIFS
AC:	P46072
Organism:	Aliivibrio fischeri
Reign:	Bacteria
TaxID:	668
EC Number:	1.6.99

Chains:

Chain Name:	Percentage of Residues within binding site
A	36 %
B	64 %

Ligand binding site composition:

B-Factor:	15.703
Number of residues:	41
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.406	904.500

% Hydrophobic	% Polar
35.07	64.93
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	71.06 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
62.457	2.24645	17.3709

Binding mode :

What is Poseview ?

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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
O2P	NH2	ARG- 12	2.96	170.71	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 12	2.96	154.05	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 12	3.7	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 12	3.91	0	Ionic (Protein Cationic)	false
C1'	CG2	THR- 14	3.73	0	Hydrophobic	false
C3'	CB	THR- 14	4.25	0	Hydrophobic	false
O1P	N	THR- 14	2.99	154.29	H-Bond (Protein Donor)	false
O2P	OG1	THR- 14	2.67	149.02	H-Bond (Protein Donor)	false
O2	NZ	LYS- 16	2.79	149.78	H-Bond (Protein Donor)	false
C8M	CB	ALA- 40	4.12	0	Hydrophobic	false
C5'	CB	ALA- 40	4.48	0	Hydrophobic	false
C7	CB	SER- 42	3.81	0	Hydrophobic	false
C4'	CB	ASN- 44	3.89	0	Hydrophobic	false
N3	OD1	ASN- 73	3.06	162.47	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 73	2.94	160.74	H-Bond (Protein Donor)	false
C7M	CE2	TYR- 144	3.76	0	Hydrophobic	false
C8M	CD1	LEU- 145	3.43	0	Hydrophobic	false
C9	CB	THR- 163	3.68	0	Hydrophobic	false
C8	CG2	THR- 163	3.58	0	Hydrophobic	false
O4	N	GLU- 165	3.18	130.55	H-Bond (Protein Donor)	false
N5	N	GLU- 165	3.15	150.14	H-Bond (Protein Donor)	false
C6	CG	GLU- 165	3.63	0	Hydrophobic	false
O4	N	GLY- 166	3.05	148.31	H-Bond (Protein Donor)	false
C7M	CG2	VAL- 187	4.36	0	Hydrophobic	false
O1P	NZ	LYS- 206	3.66	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 206	2.83	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 206	2.83	150.87	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 208	2.72	175.31	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 208	3.56	0	Ionic (Protein Cationic)	false
O2	O	HOH- 489	2.88	155.73	H-Bond (Protein Donor)	false