scPDB - 3q30 entry

Protein Data Bank Entry:

PDB ID : 3q30

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-12-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Squalene synthase
ID:	FDFT_HUMAN
AC:	P37268
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.21

Chains:

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

Ligand binding site composition:

B-Factor:	26.727
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
1.112	1137.375

% Hydrophobic	% Polar
48.07	51.93
According to VolSite

Ligand :

HET Code:	D61
Formula:	C36H39NO7
Molecular weight:	597.697 g/mol
DrugBank ID:	-
Buried Surface Area:	60.84 %
Polar Surface area:	127.82 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
17.7029	-5.68368	53.9648

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
C34	CD1	ILE- 58	4.41	0	Hydrophobic	false
C33	CG1	VAL- 69	4.07	0	Hydrophobic	false
C32	CB	TYR- 73	3.73	0	Hydrophobic	false
C30	CD2	TYR- 73	3.26	0	Hydrophobic	false
C31	CB	LEU- 76	4.02	0	Hydrophobic	false
C25	CB	LEU- 76	3.9	0	Hydrophobic	false
O18	NH1	ARG- 77	3.07	132.48	H-Bond (Protein Donor)	false
O18	NH2	ARG- 77	2.62	158.67	H-Bond (Protein Donor)	false
O20	NH1	ARG- 77	3.48	151.26	H-Bond (Protein Donor)	false
O37	NH1	ARG- 77	3.05	130.09	H-Bond (Protein Donor)	false
C23	CB	ASP- 80	3.59	0	Hydrophobic	false
C22	SD	MET- 150	3.98	0	Hydrophobic	false
C22	CE	MET- 154	3.84	0	Hydrophobic	false
C21	CB	VAL- 175	3.71	0	Hydrophobic	false
C8	CB	VAL- 179	3.83	0	Hydrophobic	false
C24	CG2	VAL- 179	4.03	0	Hydrophobic	false
C31	CG1	VAL- 179	3.97	0	Hydrophobic	false
C9	CG1	VAL- 179	3.65	0	Hydrophobic	false
C30	CG1	VAL- 179	3.71	0	Hydrophobic	false
C35	CD1	LEU- 183	4.42	0	Hydrophobic	false
C33	CD2	LEU- 183	3.57	0	Hydrophobic	false
C4	CD1	LEU- 183	3.49	0	Hydrophobic	false
C1	CE	MET- 207	4	0	Hydrophobic	false
C6	CB	MET- 207	4.02	0	Hydrophobic	false
C7	CB	MET- 207	4.41	0	Hydrophobic	false
C14	CB	LEU- 211	4.38	0	Hydrophobic	false
C12	CD1	LEU- 211	3.78	0	Hydrophobic	false
C10	CD1	LEU- 211	3.8	0	Hydrophobic	false
N16	OE1	GLN- 212	3.01	156.26	H-Bond (Ligand Donor)	false
O44	NE2	GLN- 212	3.09	154.72	H-Bond (Protein Donor)	false
C2	CE1	PHE- 288	3.46	0	Hydrophobic	false
C34	CZ	PHE- 288	3.48	0	Hydrophobic	false
C1	SG	CYS- 289	3.71	0	Hydrophobic	false
C3	CG	PRO- 292	4.28	0	Hydrophobic	false
O43	MG	MG- 600	2.2	0	Metal Acceptor	false
O37	MG	MG- 601	2.37	0	Metal Acceptor	false
O41	MG	MG- 601	2.15	0	Metal Acceptor	false
O43	MG	MG- 601	2.13	0	Metal Acceptor	false