scPDB - 2opm entry

Protein Data Bank Entry:

PDB ID : 2opm

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2007-01-29

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:	43.914
Number of residues:	32
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.670	985.500

% Hydrophobic	% Polar
47.26	52.74
According to VolSite

Ligand :

HET Code:	NI9
Formula:	C7H7FNO7P2
Molecular weight:	298.079 g/mol
DrugBank ID:	-
Buried Surface Area:	68.32 %
Polar Surface area:	170.11 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:	4

Mass center Coordinates

X	Y	Z
15.1584	79.0007	25.0799

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
F	CB	PHE- 113	4.27	0	Hydrophobic	false
F	CB	ASP- 117	4.36	0	Hydrophobic	false
O1	NH1	ARG- 126	2.98	152.45	H-Bond (Protein Donor)	false
O1	NH2	ARG- 126	3.34	135.63	H-Bond (Protein Donor)	false
O1	CZ	ARG- 126	3.58	0	Ionic (Protein Cationic)	false
F	CG2	THR- 181	4.15	0	Hydrophobic	false
C4	CG2	THR- 181	3.98	0	Hydrophobic	false
F	CG	GLN- 185	3.59	0	Hydrophobic	false
O6	NZ	LYS- 214	3.46	138.47	H-Bond (Protein Donor)	false
O6	NZ	LYS- 214	3.46	0	Ionic (Protein Cationic)	false
C6	CD	LYS- 214	3.3	0	Hydrophobic	false
C6	CB	THR- 215	4.16	0	Hydrophobic	false
O2	NE2	GLN- 254	3.18	143.8	H-Bond (Protein Donor)	false
O1	NZ	LYS- 271	3.88	0	Ionic (Protein Cationic)	false
O5	NZ	LYS- 271	2.79	0	Ionic (Protein Cationic)	false
O5	NZ	LYS- 271	2.79	150.46	H-Bond (Protein Donor)	false
O3	MG	MG- 907	2.16	0	Metal Acceptor	false
O7	MG	MG- 907	2.59	0	Metal Acceptor	false
O5	MG	MG- 908	2.24	0	Metal Acceptor	false
O6	MG	MG- 908	2.56	0	Metal Acceptor	false
O7	MG	MG- 909	2.11	0	Metal Acceptor	false