scPDB - 2e98 entry

Protein Data Bank Entry:

PDB ID : 2e98

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-01-24

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:	30.492
Number of residues:	37
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	3
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.692	1836.000

% Hydrophobic	% Polar
50.55	49.45
According to VolSite

Ligand :

HET Code:	B29
Formula:	C20H14O8P2
Molecular weight:	444.268 g/mol
DrugBank ID:	DB07410
Buried Surface Area:	63.15 %
Polar Surface area:	179.37 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
40.6269	38.5149	56.2413

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
CAO	CE	MET- 25	3.64	0	Hydrophobic	false
CAJ	CB	MET- 25	3.6	0	Hydrophobic	false
OAG	N	GLY- 27	3.18	124.08	H-Bond (Protein Donor)	false
CBB	CB	ASN- 28	4.28	0	Hydrophobic	false
OAG	ND2	ASN- 28	2.74	150.62	H-Bond (Protein Donor)	false
OAG	N	ASN- 28	2.85	149.15	H-Bond (Protein Donor)	false
OAB	N	GLY- 29	2.89	156.81	H-Bond (Protein Donor)	false
OAA	NE2	HIS- 43	2.55	163.47	H-Bond (Protein Donor)	false
CAN	CB	HIS- 43	4.43	0	Hydrophobic	false
CAQ	CB	ALA- 47	3.77	0	Hydrophobic	false
CAI	CG1	VAL- 50	4.27	0	Hydrophobic	false
CAY	CG2	VAL- 50	3.77	0	Hydrophobic	false
CAJ	CB	ALA- 69	3.57	0	Hydrophobic	false
CAS	CB	SER- 71	4.44	0	Hydrophobic	false
OAD	OG	SER- 71	2.6	166.26	H-Bond (Protein Donor)	false
OAF	OG	SER- 72	3.08	155.35	H-Bond (Protein Donor)	false
OAF	N	SER- 72	3	159.34	H-Bond (Protein Donor)	false
OAD	N	GLU- 73	2.94	160.92	H-Bond (Protein Donor)	false
OAA	CZ	ARG- 77	3.66	0	Ionic (Protein Cationic)	false
OAA	NH2	ARG- 77	2.91	169.84	H-Bond (Protein Donor)	false
CAI	CD1	ILE- 141	4.13	0	Hydrophobic	false
CAH	CG2	ILE- 141	3.8	0	Hydrophobic	false