scPDB - 3w78 entry

Protein Data Bank Entry:

PDB ID : 3w78

Resolution :2.620 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:	C0STY1_9BACI
AC:	C0STY1
Organism:	Bacillus sp. B29
Reign:	Bacteria
TaxID:	391699
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	52 %
B	48 %

Ligand binding site composition:

B-Factor:	50.713
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FMN
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.380	992.250

% Hydrophobic	% Polar
57.14	42.86
According to VolSite

Ligand :

HET Code:	CBD
Formula:	C29H17ClN7O11S3
Molecular weight:	771.134 g/mol
DrugBank ID:	DB02633
Buried Surface Area:	53.9 %
Polar Surface area:	331.65 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	4
Rings:	6
Aromatic rings:	5
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-85.6252	16.861	-11.9092

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
C7	CB	ASN- 104	4.17	0	Hydrophobic	false
C7	CB	ALA- 119	3.59	0	Hydrophobic	false
C6	CE2	PHE- 125	3.4	0	Hydrophobic	false
CB6	CG	PRO- 132	3.91	0	Hydrophobic	false
O1D	N	VAL- 150	3.27	125.98	H-Bond (Protein Donor)	false
C8	CE2	PHE- 172	3.27	0	Hydrophobic	false
CB3	CB	ASN- 187	3.73	0	Hydrophobic	false
C2	C8M	FMN- 301	4.26	0	Hydrophobic	false
C14	C1'	FMN- 301	3.6	0	Hydrophobic	false
C13	C1'	FMN- 301	3.62	0	Hydrophobic	false
NB	N1	FMN- 301	3.46	141.84	H-Bond (Ligand Donor)	false