scPDB - 3stu entry

Protein Data Bank Entry:

PDB ID : 3stu

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2011-07-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylketone synthase I
ID:	E0YCS2_SOLHA
AC:	E0YCS2
Organism:	Lycopersicon hirsutum f. glabratum
Reign:	Eukaryota
TaxID:	283673
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	28.911
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.906	567.000

% Hydrophobic	% Polar
68.45	31.55
According to VolSite

Ligand :

HET Code:	DK3
Formula:	C13H26O3
Molecular weight:	230.344 g/mol
DrugBank ID:	-
Buried Surface Area:	57.26 %
Polar Surface area:	46.53 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-35.0723	-3.30069	6.41913

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
C13	CG2	THR- 18	3.91	0	Hydrophobic	false
O2	OG1	THR- 18	2.59	168.84	H-Bond (Protein Donor)	false
C5	CB	ALA- 19	4.1	0	Hydrophobic	false
C13	CD2	PHE- 20	3.69	0	Hydrophobic	false
C3	CB	ALA- 87	4.45	0	Hydrophobic	false
C6	CD1	LEU- 88	4.41	0	Hydrophobic	false
C9	CD1	LEU- 88	4.23	0	Hydrophobic	false
C12	CB	CYS- 125	3.84	0	Hydrophobic	false
C6	CB	ALA- 128	3.87	0	Hydrophobic	false
C5	CG2	VAL- 132	3.76	0	Hydrophobic	false
C2	CG2	VAL- 132	3.65	0	Hydrophobic	false
C13	CG1	VAL- 164	4.38	0	Hydrophobic	false
C7	CD2	LEU- 183	4.18	0	Hydrophobic	false
C9	CD2	LEU- 183	4.02	0	Hydrophobic	false
C10	CD2	LEU- 185	4.28	0	Hydrophobic	false
C11	CD1	ILE- 191	3.85	0	Hydrophobic	false
C3	CD2	LEU- 218	4.31	0	Hydrophobic	false
O2	NE2	HIS- 243	3.03	156.69	H-Bond (Protein Donor)	false