scPDB - 4ga3 entry

Protein Data Bank Entry:

PDB ID : 4ga3

Resolution :2.390 Å

Experimental Method : X-ray

Deposition Date : 2012-07-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Farnesyl pyrophosphate synthase
ID:	FPPS_HUMAN
AC:	P14324
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.10

Chains:

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

Ligand binding site composition:

B-Factor:	28.955
Number of residues:	37
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	3
Water Molecules:	5
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.092	313.875

% Hydrophobic	% Polar
44.09	55.91
According to VolSite

Ligand :

HET Code:	4GA
Formula:	C9H15N2O7P2
Molecular weight:	325.172 g/mol
DrugBank ID:	-
Buried Surface Area:	68.18 %
Polar Surface area:	175.04 Å2

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

Mass center Coordinates

X	Y	Z
15.8899	79.1	25.7151

Binding mode :

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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
CAL	CB	PHE- 99	3.41	0	Hydrophobic	false
CAA	CB	ASP- 103	4.45	0	Hydrophobic	false
OAB	CZ	ARG- 112	3.96	0	Ionic (Protein Cationic)	false
OAF	CZ	ARG- 112	3.35	0	Ionic (Protein Cationic)	false
OAB	NH2	ARG- 112	3.06	139.94	H-Bond (Protein Donor)	false
OAF	NH2	ARG- 112	3.24	128.67	H-Bond (Protein Donor)	false
OAF	NH1	ARG- 112	2.63	161.55	H-Bond (Protein Donor)	false
CAA	CG	GLN- 171	4.11	0	Hydrophobic	false
OAC	NZ	LYS- 200	2.61	144.2	H-Bond (Protein Donor)	false
OAC	NZ	LYS- 200	2.61	0	Ionic (Protein Cationic)	false
OAG	NZ	LYS- 200	3.84	0	Ionic (Protein Cationic)	false
CAN	CB	LYS- 200	4.08	0	Hydrophobic	false
CAN	CE1	TYR- 204	4.11	0	Hydrophobic	false
OAD	NE2	GLN- 240	3.07	166.62	H-Bond (Protein Donor)	false
OAD	OD1	ASP- 243	3.31	166.58	H-Bond (Ligand Donor)	false
OAE	NZ	LYS- 257	2.92	146.58	H-Bond (Protein Donor)	false
OAF	NZ	LYS- 257	3.33	141.87	H-Bond (Protein Donor)	false
OAE	NZ	LYS- 257	2.92	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 257	3.33	0	Ionic (Protein Cationic)	false
OAD	MG	MG- 1002	2.15	0	Metal Acceptor	false
OAE	MG	MG- 1002	2.19	0	Metal Acceptor	false
OAG	MG	MG- 1002	2.02	0	Metal Acceptor	false
OAH	MG	MG- 1003	2.07	0	Metal Acceptor	false
OAB	MG	MG- 1004	2	0	Metal Acceptor	false
OAH	MG	MG- 1004	2.02	0	Metal Acceptor	false