scPDB - 1x09 entry

Protein Data Bank Entry:

PDB ID : 1x09

Resolution :1.870 Å

Experimental Method : X-ray

Deposition Date : 2005-03-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
ID:	UPPS_ECOLI
AC:	P60472
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.5.1.31

Chains:

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

Ligand binding site composition:

B-Factor:	23.142
Number of residues:	22
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.992	948.375

% Hydrophobic	% Polar
54.09	45.91
According to VolSite

Ligand :

HET Code:	IPE
Formula:	C5H9O7P2
Molecular weight:	243.068 g/mol
DrugBank ID:	DB04714
Buried Surface Area:	60.15 %
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
23.819	13.3868	19.0149

Binding mode :

What is Poseview ?

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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
C1	CG2	ILE- 24	4.25	0	Hydrophobic	false
C4	CG2	ILE- 24	3.76	0	Hydrophobic	false
C4	CB	ALA- 26	3.98	0	Hydrophobic	false
C1	CE1	TYR- 68	3.93	0	Hydrophobic	false
C5	CG	TYR- 68	3.92	0	Hydrophobic	false
O2A	ND2	ASN- 74	2.78	168.54	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 194	3.08	146.94	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 200	3.45	125.21	H-Bond (Protein Donor)	false
O1B	NE	ARG- 200	2.71	155.71	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 200	2.79	172.95	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 200	3.5	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 200	3.7	0	Ionic (Protein Cationic)	false
C1	CB	SER- 202	3.94	0	Hydrophobic	false
O1B	OG	SER- 202	2.67	152.94	H-Bond (Protein Donor)	false
O1A	MG	MG- 900	1.98	0	Metal Acceptor	false
O3B	MG	MG- 900	2.17	0	Metal Acceptor	false