scPDB - 2fre entry

Protein Data Bank Entry:

PDB ID : 2fre

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2006-01-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)H-flavin oxidoreductase
ID:	A9CKT4_AGRFC
AC:	A9CKT4
Organism:	Agrobacterium fabrum )
Reign:	Bacteria
TaxID:	176299
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	31 %
B	69 %

Ligand binding site composition:

B-Factor:	25.786
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.118	587.250

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	70.37 %
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
24.7057	14.6367	25.3621

Binding mode :

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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
O1P	CZ	ARG- 7	3.7	0	Ionic (Protein Cationic)	false
O1P	NH2	ARG- 7	2.71	146.16	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 20	2.93	145.89	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 20	3.05	168.2	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 20	3.68	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 20	3.83	0	Ionic (Protein Cationic)	false
O2P	OG	SER- 22	2.66	156.21	H-Bond (Protein Donor)	false
O3P	N	SER- 22	2.71	140.04	H-Bond (Protein Donor)	false
O2	NE	ARG- 24	3.05	139.98	H-Bond (Protein Donor)	false
O2	NH2	ARG- 24	2.82	151.23	H-Bond (Protein Donor)	false
C8M	CB	PRO- 47	4.26	0	Hydrophobic	false
C5'	CB	PRO- 47	4.4	0	Hydrophobic	false
C6	CB	ALA- 49	3.56	0	Hydrophobic	false
C4'	CB	ASN- 51	4.06	0	Hydrophobic	false
N3	OD1	ASN- 78	2.88	130.11	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 78	3.01	162.75	H-Bond (Protein Donor)	false
C7M	CG2	THR- 109	3.97	0	Hydrophobic	false
C7M	CE2	PHE- 112	3.98	0	Hydrophobic	false
C8M	CZ2	TRP- 118	3.92	0	Hydrophobic	false
N1	NE2	HIS- 133	2.81	154.05	H-Bond (Protein Donor)	false
O2	NE2	HIS- 133	3.36	126.34	H-Bond (Protein Donor)	false
O4	N	GLY- 136	3.21	133.39	H-Bond (Protein Donor)	false
N5	N	GLY- 136	2.84	146.8	H-Bond (Protein Donor)	false
O4	N	GLY- 137	3	149.56	H-Bond (Protein Donor)	false
C7M	CB	ALA- 157	4.37	0	Hydrophobic	false
C5'	CB	SER- 181	4.25	0	Hydrophobic	false
O5'	OG	SER- 181	2.69	151.51	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 183	3.9	0	Ionic (Protein Cationic)	false
O1P	NH2	ARG- 183	2.89	162.37	H-Bond (Protein Donor)	false
O3'	O	HOH- 1165	2.99	142.14	H-Bond (Protein Donor)	false
O2	O	HOH- 1235	2.74	179.96	H-Bond (Protein Donor)	false