scPDB - 3d74 entry

Protein Data Bank Entry:

PDB ID : 3d74

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2008-05-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pheromone-binding protein ASP1
ID:	Q9U9J6_APIME
AC:	Q9U9J6
Organism:	Apis mellifera
Reign:	Eukaryota
TaxID:	7460
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.803
Number of residues:	20
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.907	465.750

% Hydrophobic	% Polar
78.99	21.01
According to VolSite

Ligand :

HET Code:	NBB
Formula:	C10H15NO2S
Molecular weight:	213.297 g/mol
DrugBank ID:	DB02055
Buried Surface Area:	53.43 %
Polar Surface area:	54.55 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
24.2121	31.8514	-22.2238

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
C12	CG	PRO- 6	4.13	0	Hydrophobic	false
C11	CG2	VAL- 9	4.2	0	Hydrophobic	false
C5	CG2	VAL- 9	4.25	0	Hydrophobic	false
C13	CD2	LEU- 12	4.4	0	Hydrophobic	false
C14	CG	LEU- 12	4.39	0	Hydrophobic	false
C1	CD1	LEU- 58	3.61	0	Hydrophobic	false
C2	CG	MET- 70	4.15	0	Hydrophobic	false
N10	O	LEU- 73	2.7	157.23	H-Bond (Ligand Donor)	false
C11	CB	LEU- 73	4.06	0	Hydrophobic	false
C13	CD2	LEU- 73	4.37	0	Hydrophobic	false
C3	CB	LEU- 73	3.68	0	Hydrophobic	false
C3	CD2	LEU- 74	3.6	0	Hydrophobic	false