scPDB - 2vqb entry

Protein Data Bank Entry:

PDB ID : 2vqb

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2008-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative flavin-containing monooxygenase
ID:	Q83XK4_9GAMM
AC:	Q83XK4
Organism:	Methylophaga aminisulfidivorans
Reign:	Bacteria
TaxID:	230105
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	51.693
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.641	688.500

% Hydrophobic	% Polar
47.06	52.94
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	65.08 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-22.5166	229.232	23.7337

Binding mode :

What is Poseview ?

2D View
3D View

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
C4N	CD1	LEU- 75	4.17	0	Hydrophobic	false
N7N	O	TRP- 76	3.27	155.56	H-Bond (Ligand Donor)	false
O2D	ND2	ASN- 78	3.28	162.18	H-Bond (Protein Donor)	false
C3N	CB	ASN- 78	4.45	0	Hydrophobic	false
C3D	CZ	PHE- 170	4.14	0	Hydrophobic	false
C5D	CE1	PHE- 170	3.79	0	Hydrophobic	false
O3B	N	SER- 210	3.07	145.56	H-Bond (Protein Donor)	false
O3B	OG	SER- 210	3.13	164.13	H-Bond (Protein Donor)	false
O1A	OG	SER- 211	3.12	177.94	H-Bond (Protein Donor)	false
C4B	CB	SER- 211	3.81	0	Hydrophobic	false
C2D	CD2	TYR- 212	3.54	0	Hydrophobic	false
O1N	N	SER- 213	2.97	176.14	H-Bond (Protein Donor)	false
O2N	OG	SER- 213	2.6	150.5	H-Bond (Protein Donor)	false
C5N	CB	SER- 213	4.13	0	Hydrophobic	false
C4N	CB	ASP- 216	3.96	0	Hydrophobic	false
O2X	CZ	ARG- 234	3.86	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 234	3.89	0	Ionic (Protein Cationic)	false
O2X	NE	ARG- 234	3.24	140.62	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 234	2.86	146.41	H-Bond (Protein Donor)	false
O2X	OG1	THR- 235	2.57	143.47	H-Bond (Protein Donor)	false
N1A	ND2	ASN- 251	3.47	157.39	H-Bond (Protein Donor)	false
C1B	CG2	THR- 277	4.41	0	Hydrophobic	false
C4D	C9	FAD- 500	4.48	0	Hydrophobic	false
C5N	C7M	FAD- 500	3.86	0	Hydrophobic	false
N7N	N5	FAD- 500	3.04	176.38	H-Bond (Ligand Donor)	false