scPDB - 2v5z entry

Protein Data Bank Entry:

PDB ID : 2v5z

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2007-07-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Amine oxidase [flavin-containing] B
ID:	AOFB_HUMAN
AC:	P27338
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.4.3.4

Chains:

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

Ligand binding site composition:

B-Factor:	14.034
Number of residues:	38
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.297	313.875

% Hydrophobic	% Polar
64.52	35.48
According to VolSite

Ligand :

HET Code:	SAG
Formula:	C17H17FN2O2
Molecular weight:	300.327 g/mol
DrugBank ID:	DB08516
Buried Surface Area:	74.18 %
Polar Surface area:	64.67 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
15.6328	129.034	23.6464

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
F3	CH2	TRP- 119	3.62	0	Hydrophobic	false
F3	CD1	LEU- 164	3.43	0	Hydrophobic	false
F3	CD2	LEU- 167	4.22	0	Hydrophobic	false
C2	CD2	LEU- 167	4.46	0	Hydrophobic	false
F3	CB	PHE- 168	3.81	0	Hydrophobic	false
C7	CD2	LEU- 171	3.63	0	Hydrophobic	false
C9	CD2	LEU- 171	3.54	0	Hydrophobic	false
C11	CG	LEU- 171	4.14	0	Hydrophobic	false
C14	CG	LEU- 171	4.04	0	Hydrophobic	false
C14	SG	CYS- 172	3.64	0	Hydrophobic	false
C13	CG1	ILE- 198	4.44	0	Hydrophobic	false
C2	CG2	ILE- 199	4.1	0	Hydrophobic	false
C5	CD1	ILE- 199	3.88	0	Hydrophobic	false
C1	CB	ILE- 199	3.78	0	Hydrophobic	false
C9	CG2	ILE- 199	4.16	0	Hydrophobic	false
C11	CG	GLN- 206	4.11	0	Hydrophobic	false
N21	OE1	GLN- 206	2.81	133.7	H-Bond (Ligand Donor)	false
C5	CD1	ILE- 316	3.7	0	Hydrophobic	false
C7	CE1	TYR- 326	3.69	0	Hydrophobic	false
C18	CZ	PHE- 343	3.71	0	Hydrophobic	false
C18	CZ	TYR- 398	3.7	0	Hydrophobic	false
N21	O	HOH- 1192	3.37	159.74	H-Bond (Ligand Donor)	false