scPDB - 1yxq entry

Protein Data Bank Entry:

PDB ID : 1yxq

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2005-02-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Actin, alpha skeletal muscle
ID:	ACTS_RABIT
AC:	P68135
Organism:	Oryctolagus cuniculus
Reign:	Eukaryota
TaxID:	9986
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	49 %
B	51 %

Ligand binding site composition:

B-Factor:	21.033
Number of residues:	59
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.344	1360.125

% Hydrophobic	% Polar
34.24	65.76
According to VolSite

Ligand :

HET Code:	SWI
Formula:	C78H132O20
Molecular weight:	1389.871 g/mol
DrugBank ID:	-
Buried Surface Area:	50.95 %
Polar Surface area:	288.28 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	8
Rings:	5
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	4
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
10.8449	-5.98257	20.5994

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
C9	CB	ASP- 25	4.19	0	Hydrophobic	false
C48	CB	ASP- 25	4.11	0	Hydrophobic	false
C78	CZ	TYR- 133	4.47	0	Hydrophobic	false
C24	CG	TYR- 143	3.73	0	Hydrophobic	false
C29	CZ	TYR- 143	4.29	0	Hydrophobic	false
C37	CB	TYR- 143	3.54	0	Hydrophobic	false
C75	CB	TYR- 143	4.48	0	Hydrophobic	false
C64	CD2	TYR- 143	4.14	0	Hydrophobic	false
C65	CZ	TYR- 143	3.79	0	Hydrophobic	false
C67	CZ	TYR- 143	4.22	0	Hydrophobic	false
C78	CZ	TYR- 143	4.41	0	Hydrophobic	false
C28	CZ	TYR- 143	4.01	0	Hydrophobic	false
C76	CG	TYR- 143	3.46	0	Hydrophobic	false
O2	O	SER- 145	2.95	152.02	H-Bond (Ligand Donor)	false
O12	O	SER- 145	3.06	169.4	H-Bond (Ligand Donor)	false
O5	O	GLY- 146	2.58	164.46	H-Bond (Ligand Donor)	false
O15	O	GLY- 146	2.63	164.96	H-Bond (Ligand Donor)	false
C38	CG	ARG- 147	4.33	0	Hydrophobic	false
C77	CG	ARG- 147	4.33	0	Hydrophobic	false
C27	CG2	THR- 148	4.27	0	Hydrophobic	false
C75	CG2	THR- 148	4.17	0	Hydrophobic	false
C64	CG2	THR- 148	4.09	0	Hydrophobic	false
C23	CG2	THR- 148	4.36	0	Hydrophobic	false
C39	CZ	TYR- 169	3.58	0	Hydrophobic	false
C12	CB	SER- 344	4.21	0	Hydrophobic	false
C51	CB	SER- 344	4.13	0	Hydrophobic	false
C37	CG2	ILE- 345	4.07	0	Hydrophobic	false
C36	CG2	ILE- 345	3.88	0	Hydrophobic	false
C18	CG2	ILE- 345	4.41	0	Hydrophobic	false
C13	CG1	ILE- 345	4	0	Hydrophobic	false
C8	CG1	ILE- 345	4.13	0	Hydrophobic	false
C33	CD1	ILE- 345	4.06	0	Hydrophobic	false
C72	CD1	ILE- 345	4.22	0	Hydrophobic	false
C57	CG2	ILE- 345	4.45	0	Hydrophobic	false
C76	CG2	ILE- 345	4.31	0	Hydrophobic	false
C47	CG1	ILE- 345	4	0	Hydrophobic	false
C52	CG1	ILE- 345	3.85	0	Hydrophobic	false
C76	CD1	LEU- 346	4.32	0	Hydrophobic	false
C65	CD1	LEU- 346	4.47	0	Hydrophobic	false
C29	CD1	LEU- 346	3.92	0	Hydrophobic	false
C68	CD1	LEU- 346	3.97	0	Hydrophobic	false
C34	CB	SER- 348	3.6	0	Hydrophobic	false
C73	CB	SER- 348	3.7	0	Hydrophobic	false
C37	CD1	LEU- 349	4.22	0	Hydrophobic	false
C36	CD1	LEU- 349	3.52	0	Hydrophobic	false
C18	CD2	LEU- 349	4.09	0	Hydrophobic	false
C57	CD2	LEU- 349	4.29	0	Hydrophobic	false
C32	CD1	LEU- 349	3.93	0	Hydrophobic	false
C63	CD1	LEU- 349	3.86	0	Hydrophobic	false
C71	CD1	LEU- 349	3.99	0	Hydrophobic	false
C32	CB	THR- 351	4.03	0	Hydrophobic	false
C71	CB	THR- 351	3.95	0	Hydrophobic	false
C69	CD1	PHE- 352	4.49	0	Hydrophobic	false
C30	SD	MET- 355	3.7	0	Hydrophobic	false
C39	CE	MET- 355	3.98	0	Hydrophobic	false
C69	SD	MET- 355	3.69	0	Hydrophobic	false
C78	CE	MET- 355	4.22	0	Hydrophobic	false