scPDB - 2e9a entry

Protein Data Bank Entry:

PDB ID : 2e9a

Resolution :2.100 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:	48.899
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.610	999.000

% Hydrophobic	% Polar
63.85	36.15
According to VolSite

Ligand :

HET Code:	B28
Formula:	C20H16O7P2
Molecular weight:	430.284 g/mol
DrugBank ID:	DB07409
Buried Surface Area:	56.88 %
Polar Surface area:	166.23 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
40.8561	38.98	57.4634

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
CAK	CB	MET- 25	3.63	0	Hydrophobic	false
CBA	CB	ASN- 28	4.18	0	Hydrophobic	false
OAF	N	ASN- 28	2.98	143.91	H-Bond (Protein Donor)	false
OAC	ND2	ASN- 28	3.28	153.34	H-Bond (Protein Donor)	false
OAG	N	GLY- 29	2.53	144.56	H-Bond (Protein Donor)	false
OAD	NE	ARG- 39	2.78	138.51	H-Bond (Protein Donor)	false
OAD	CZ	ARG- 39	3.82	0	Ionic (Protein Cationic)	false
OAE	NE2	HIS- 43	2.77	154.1	H-Bond (Protein Donor)	false
CAS	CB	HIS- 43	4.44	0	Hydrophobic	false
CAN	CB	ALA- 47	3.48	0	Hydrophobic	false
CAW	CB	ALA- 47	3.35	0	Hydrophobic	false
CAP	CG2	VAL- 50	4	0	Hydrophobic	false
CAK	CB	ALA- 69	3.44	0	Hydrophobic	false
OAA	OG	SER- 71	2.82	157.95	H-Bond (Protein Donor)	false
OAA	N	SER- 72	3.32	140.49	H-Bond (Protein Donor)	false
OAG	OG	SER- 72	3.48	132.42	H-Bond (Protein Donor)	false
OAB	N	SER- 72	3.24	142.41	H-Bond (Protein Donor)	false
OAB	OG	SER- 72	3.03	153.7	H-Bond (Protein Donor)	false
CAJ	CB	ALA- 92	4.04	0	Hydrophobic	false
CAH	CG	GLU- 96	4.05	0	Hydrophobic	false