scPDB - 3w77 entry

Protein Data Bank Entry:

PDB ID : 3w77

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2013-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FMN-dependent NADH-azoreductase
ID:	Q0WXX2_9BACI
AC:	Q0WXX2
Organism:	Bacillus sp. B29
Reign:	Bacteria
TaxID:	391699
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	14 %
B	86 %

Ligand binding site composition:

B-Factor:	15.312
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.860	482.625

% Hydrophobic	% Polar
41.26	58.74
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	66.73 %
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
31.0584	39.0876	66.6251

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
O3P	ND2	ASN- 10	2.94	154.91	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 12	3.88	0	Ionic (Protein Cationic)	false
O3P	NH1	ARG- 12	2.85	144.53	H-Bond (Protein Donor)	false
O2P	N	VAL- 18	3.39	133.16	H-Bond (Protein Donor)	false
O1P	OG	SER- 19	2.58	155.03	H-Bond (Protein Donor)	false
O1P	N	SER- 19	2.92	155.29	H-Bond (Protein Donor)	false
C7M	CG1	ILE- 57	4.13	0	Hydrophobic	false
C8M	CG2	ILE- 57	3.7	0	Hydrophobic	false
C5'	CB	PRO- 98	3.28	0	Hydrophobic	false
O2'	O	LEU- 99	2.73	165	H-Bond (Ligand Donor)	false
C8M	CE2	TRP- 100	4.33	0	Hydrophobic	false
C6	CB	TRP- 100	3.58	0	Hydrophobic	false
O5'	NE1	TRP- 100	3.43	136.29	H-Bond (Protein Donor)	false
O3P	NE1	TRP- 100	3.18	154.47	H-Bond (Protein Donor)	false
N5	N	ASN- 101	2.85	174.19	H-Bond (Protein Donor)	false
O4	N	LEU- 102	3.11	145.83	H-Bond (Protein Donor)	false
C4'	CB	ALA- 143	4.02	0	Hydrophobic	false
O2'	N	GLY- 145	2.97	132.28	H-Bond (Protein Donor)	false
O2	N	GLY- 146	2.83	145.22	H-Bond (Protein Donor)	false
N3	OH	TYR- 148	2.84	159.86	H-Bond (Ligand Donor)	false