scPDB - 1rqj entry

Protein Data Bank Entry:

PDB ID : 1rqj

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2003-12-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Farnesyl diphosphate synthase
ID:	ISPA_ECOLI
AC:	P22939
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.5.1.10

Chains:

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

Ligand binding site composition:

B-Factor:	21.858
Number of residues:	29
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.264	641.250

% Hydrophobic	% Polar
37.37	62.63
According to VolSite

Ligand :

HET Code:	IPE
Formula:	C5H9O7P2
Molecular weight:	243.068 g/mol
DrugBank ID:	DB04714
Buried Surface Area:	64.96 %
Polar Surface area:	141.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
60.3089	67.5943	8.92171

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
O1A	NZ	LYS- 66	2.79	160.38	H-Bond (Protein Donor)	false
O2B	N	LYS- 66	2.93	164.38	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 66	2.59	151.26	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 66	2.79	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 66	3.56	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 66	2.59	0	Ionic (Protein Cationic)	false
O1	NH1	ARG- 69	3.47	134.83	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 69	2.88	165.87	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 69	3.83	0	Ionic (Protein Cationic)	false
O3B	NE2	HIS- 98	2.98	146.96	H-Bond (Protein Donor)	false
C2	CD2	LEU- 102	3.71	0	Hydrophobic	false
O1B	CZ	ARG- 117	3.74	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 117	3.76	0	Ionic (Protein Cationic)	false
O1B	NE	ARG- 117	2.93	178.68	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 117	2.84	164.16	H-Bond (Protein Donor)	false
C5	CG2	THR- 203	4.19	0	Hydrophobic	false
C5	CE2	PHE- 240	3.48	0	Hydrophobic	false
C5	CB	ASP- 244	3.85	0	Hydrophobic	false
O3B	O	HOH- 912	2.65	179.97	H-Bond (Protein Donor)	false
O1A	O	HOH- 913	2.76	148.65	H-Bond (Protein Donor)	false