scPDB - 3eks entry

Protein Data Bank Entry:

PDB ID : 3eks

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2008-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Actin-5C
ID:	ACT1_DROME
AC:	P10987
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.440
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.372	600.750

% Hydrophobic	% Polar
53.37	46.63
According to VolSite

Ligand :

HET Code:	CY9
Formula:	C30H37NO6
Molecular weight:	507.618 g/mol
DrugBank ID:	-
Buried Surface Area:	57.53 %
Polar Surface area:	112.93 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
157.906	-16.4022	31.948

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
C5	CE2	TYR- 133	4.26	0	Hydrophobic	false
C11	CZ	TYR- 133	4.15	0	Hydrophobic	false
C7	CB	ILE- 136	4.4	0	Hydrophobic	false
C15	CG1	ILE- 136	4.03	0	Hydrophobic	false
C16	CD1	ILE- 136	4.45	0	Hydrophobic	false
O7	N	ILE- 136	2.87	159.9	H-Bond (Protein Donor)	false
C7	CG2	VAL- 139	4.18	0	Hydrophobic	false
N2	O	GLY- 168	2.87	146.98	H-Bond (Ligand Donor)	false
C10	CE2	TYR- 169	3.97	0	Hydrophobic	false
C21	CD2	TYR- 169	3.72	0	Hydrophobic	false
O1	N	ALA- 170	2.94	146.5	H-Bond (Protein Donor)	false
O18	O	ALA- 170	3.08	154.22	H-Bond (Ligand Donor)	false
C22	CG	PRO- 172	3.43	0	Hydrophobic	false
C23	CG	PRO- 172	4.25	0	Hydrophobic	false
C11	CD2	LEU- 346	3.92	0	Hydrophobic	false
C26	CD1	LEU- 346	4.13	0	Hydrophobic	false
C26	CB	PHE- 352	4.45	0	Hydrophobic	false
C11	CE2	PHE- 352	4.28	0	Hydrophobic	false
C29	CE	MET- 355	4.3	0	Hydrophobic	false
C31	CE	MET- 355	3.8	0	Hydrophobic	false
C28	CG	MET- 355	3.62	0	Hydrophobic	false
C16	CB	PHE- 375	3.6	0	Hydrophobic	false
O7	O	HOH- 1076	3.02	161.68	H-Bond (Ligand Donor)	false