scPDB - 4nbb entry

Protein Data Bank Entry:

PDB ID : 4nbb

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2013-10-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Terminal oxygenase component of carbazole
ID:	Q84II6_JANS3
AC:	Q84II6
Organism:	Janthinobacterium sp.
Reign:	Bacteria
TaxID:	213804
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.274
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.397	546.750

% Hydrophobic	% Polar
62.96	37.04
According to VolSite

Ligand :

HET Code:	9CA
Formula:	C12H9N
Molecular weight:	167.207 g/mol
DrugBank ID:	DB07301
Buried Surface Area:	61.29 %
Polar Surface area:	15.79 Å2

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

Mass center Coordinates

X	Y	Z
0.730462	23.5714	49.5731

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
N9	O	GLY- 178	2.72	162.37	H-Bond (Ligand Donor)	false
C6	CD1	ILE- 184	4.32	0	Hydrophobic	false
C5	CB	ALA- 259	3.83	0	Hydrophobic	false
C7	CG2	VAL- 262	3.85	0	Hydrophobic	false
C1	CD2	LEU- 270	3.56	0	Hydrophobic	false
C4	CG1	VAL- 272	3.89	0	Hydrophobic	false
C8A	CG2	VAL- 272	4.42	0	Hydrophobic	false
C4B	CG1	VAL- 272	4.22	0	Hydrophobic	false
C9A	CG2	VAL- 272	3.57	0	Hydrophobic	false
C3	CE2	PHE- 275	3.47	0	Hydrophobic	false