scPDB - 3vjc entry

Protein Data Bank Entry:

PDB ID : 3vjc

Resolution :1.890 Å

Experimental Method : X-ray

Deposition Date : 2011-10-14

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
B	95 %
C	5 %

Ligand binding site composition:

B-Factor:	23.495
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.109	1019.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	ZGA
Formula:	C35H43O14
Molecular weight:	687.708 g/mol
DrugBank ID:	-
Buried Surface Area:	64.28 %
Polar Surface area:	231.9 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
49.8536	37.0873	46.5183

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
OAP	O	THR- 50	2.78	120.16	H-Bond (Ligand Donor)	false
OAN	OG	SER- 51	2.69	174.19	H-Bond (Protein Donor)	false
OAJ	CZ	ARG- 52	3.58	0	Ionic (Protein Cationic)	false
OAM	CZ	ARG- 52	3.65	0	Ionic (Protein Cationic)	false
OAJ	NE	ARG- 52	3.47	129.7	H-Bond (Protein Donor)	false
OAJ	NH1	ARG- 52	2.87	148.68	H-Bond (Protein Donor)	false
OAL	NH1	ARG- 52	3.15	125.8	H-Bond (Protein Donor)	false
OAM	N	ARG- 52	3.01	156.42	H-Bond (Protein Donor)	false
OAM	NE	ARG- 52	2.84	174.51	H-Bond (Protein Donor)	false
OAH	OG	SER- 53	3.39	127.18	H-Bond (Protein Donor)	false
OAK	N	SER- 53	2.77	151	H-Bond (Protein Donor)	false
CAD	CB	SER- 53	3.68	0	Hydrophobic	false
CAD	CZ	PHE- 54	4.28	0	Hydrophobic	false
CAS	CD1	ILE- 58	4.1	0	Hydrophobic	false
CAS	CG1	VAL- 69	4.22	0	Hydrophobic	false
OAN	OH	TYR- 73	2.68	137.03	H-Bond (Protein Donor)	false
OBF	OH	TYR- 73	3.18	137.38	H-Bond (Protein Donor)	false
CBA	CD2	TYR- 73	4.43	0	Hydrophobic	false
CAF	CE2	TYR- 73	3.45	0	Hydrophobic	false
CAT	CB	TYR- 73	3.76	0	Hydrophobic	false
CAF	CB	LEU- 76	4.02	0	Hydrophobic	false
CAV	CD1	LEU- 76	4.12	0	Hydrophobic	false
CBA	CD1	LEU- 76	4.46	0	Hydrophobic	false
CAF	CB	ARG- 77	4.33	0	Hydrophobic	false
OAI	CZ	ARG- 77	3.71	0	Ionic (Protein Cationic)	false
OAI	NH2	ARG- 77	2.88	133.29	H-Bond (Protein Donor)	false
OAP	NH1	ARG- 77	2.65	158.43	H-Bond (Protein Donor)	false
CAC	CB	ASP- 80	4.25	0	Hydrophobic	false
OAI	NZ	LYS- 117	2.85	151.77	H-Bond (Protein Donor)	false
OAI	NZ	LYS- 117	2.85	0	Ionic (Protein Cationic)	false
CAC	SD	MET- 150	3.61	0	Hydrophobic	false
CAC	CE	MET- 154	4.04	0	Hydrophobic	false
CAC	CG2	VAL- 179	4.44	0	Hydrophobic	false
CAV	CG1	VAL- 179	3.63	0	Hydrophobic	false
CBM	CG1	VAL- 179	3.56	0	Hydrophobic	false
CAU	CD1	LEU- 183	4.37	0	Hydrophobic	false
CAS	CD2	LEU- 183	4.07	0	Hydrophobic	false
CAE	CD2	LEU- 211	3.89	0	Hydrophobic	false
CAB	CG2	THR- 214	3.89	0	Hydrophobic	false
CAD	CB	PRO- 292	3.74	0	Hydrophobic	false
CAD	SD	MET- 295	4.31	0	Hydrophobic	false
CAX	CB	MET- 295	4.14	0	Hydrophobic	false
CBB	CB	MET- 295	4.19	0	Hydrophobic	false
CAB	CB	ALA- 296	4.26	0	Hydrophobic	false
CAB	CB	THR- 299	4.27	0	Hydrophobic	false
CAD	CG2	VAL- 322	4.13	0	Hydrophobic	false