scPDB - 2b9y entry

Protein Data Bank Entry:

PDB ID : 2b9y

Resolution :2.210 Å

Experimental Method : X-ray

Deposition Date : 2005-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative aminooxidase
ID:	Q6A8X5_PROAC
AC:	Q6A8X5
Organism:	Propionibacterium acnes
Reign:	Bacteria
TaxID:	267747
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.422
Number of residues:	61
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.954	1056.375

% Hydrophobic	% Polar
47.92	52.08
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	74.48 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
1.21506	-26.7487	25.0322

Binding mode :

What is Poseview ?

2D View
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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
C4'	CG	PRO- 16	4.01	0	Hydrophobic	false
O1P	N	ALA- 17	2.91	155.23	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 37	2.62	154.93	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 37	2.54	153.7	H-Bond (Ligand Donor)	false
N3A	N	ARG- 38	3.18	142.96	H-Bond (Protein Donor)	false
O1A	N	LYS- 45	2.87	172.33	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 45	2.76	138.06	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 45	2.76	0	Ionic (Protein Cationic)	false
C8M	CD	LYS- 45	4	0	Hydrophobic	false
C9	CB	LYS- 45	4.07	0	Hydrophobic	false
C3'	CB	LYS- 45	4.26	0	Hydrophobic	false
C2'	CB	ALA- 60	4.24	0	Hydrophobic	false
C9A	CB	ALA- 60	3.8	0	Hydrophobic	false
N3	O	MET- 62	3.04	130.82	H-Bond (Ligand Donor)	false
O4	N	MET- 62	3.44	154.69	H-Bond (Protein Donor)	false
O2	OH	TYR- 67	3.21	139.15	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 254	4.1	0	Hydrophobic	false
C7M	CE2	TYR- 281	3.54	0	Hydrophobic	false
C7M	CG2	VAL- 283	3.47	0	Hydrophobic	false
C7M	CE1	TYR- 328	3.84	0	Hydrophobic	false
C8M	CE2	TRP- 368	3.52	0	Hydrophobic	false
C8M	CE1	TYR- 370	3.73	0	Hydrophobic	false
C1'	CE1	TYR- 370	4.18	0	Hydrophobic	false
C9	CE1	TYR- 370	3.17	0	Hydrophobic	false
O3'	OE2	GLU- 401	2.52	158.05	H-Bond (Ligand Donor)	false
C5'	CG	GLU- 401	3.77	0	Hydrophobic	false
O2	N	PHE- 408	2.95	154.2	H-Bond (Protein Donor)	false
C2'	CD2	PHE- 408	4.31	0	Hydrophobic	false
C4'	CB	PHE- 408	4.08	0	Hydrophobic	false
C5'	CG2	VAL- 411	3.94	0	Hydrophobic	false
O2P	O	HOH- 1541	2.66	179.96	H-Bond (Protein Donor)	false
O1P	O	HOH- 1544	2.65	179.97	H-Bond (Protein Donor)	false
O3B	O	HOH- 1561	2.66	179.95	H-Bond (Protein Donor)	false
N1A	O	HOH- 1614	2.79	179.99	H-Bond (Protein Donor)	false
O2B	O	HOH- 1732	2.6	179.97	H-Bond (Protein Donor)	false