scPDB - 3bfa entry

Protein Data Bank Entry:

PDB ID : 3bfa

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2007-11-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Odorant binding protein ASP1
ID:	Q8WRW5_APIME
AC:	Q8WRW5
Organism:	Apis mellifera
Reign:	Eukaryota
TaxID:	7460
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	69.686
Number of residues:	18
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.220	891.000

% Hydrophobic	% Polar
80.30	19.70
According to VolSite

Ligand :

HET Code:	9OD
Formula:	C10H15O3
Molecular weight:	183.224 g/mol
DrugBank ID:	-
Buried Surface Area:	54.33 %
Polar Surface area:	57.2 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
17.6605	11.8725	-2.52069

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
C5	CG1	VAL- 13	3.97	0	Hydrophobic	false
C10	CG	MET- 49	4.21	0	Hydrophobic	false
C7	CD2	LEU- 52	3.78	0	Hydrophobic	false
C10	CG	LEU- 53	4.35	0	Hydrophobic	false
C8	CD2	LEU- 53	4.12	0	Hydrophobic	false
C5	CD2	PHE- 56	3.75	0	Hydrophobic	false
C4	CG	PHE- 56	4.26	0	Hydrophobic	false
C6	CD1	LEU- 58	3.84	0	Hydrophobic	false
C4	CD2	LEU- 73	4.25	0	Hydrophobic	false
C10	CG2	VAL- 118	3.62	0	Hydrophobic	false
O9	N	ILE- 119	2.74	140	H-Bond (Protein Donor)	false