scPDB - 2e9c entry

Protein Data Bank Entry:

PDB ID : 2e9c

Resolution :2.050 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
B	100 %

Ligand binding site composition:

B-Factor:	41.935
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.311	1458.000

% Hydrophobic	% Polar
57.64	42.36
According to VolSite

Ligand :

HET Code:	B75
Formula:	C24H19NO9P2S
Molecular weight:	559.421 g/mol
DrugBank ID:	-
Buried Surface Area:	43.25 %
Polar Surface area:	220.78 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	4
Aromatic rings:	4
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
8.42814	34.6164	28.5996

Binding mode :

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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
CAP	CE	MET- 25	3.57	0	Hydrophobic	false
CAJ	CB	MET- 25	3.86	0	Hydrophobic	false
CAW	CE	MET- 25	3.63	0	Hydrophobic	false
OAI	N	GLY- 27	3.16	128.68	H-Bond (Protein Donor)	false
CBH	CB	ASN- 28	4.02	0	Hydrophobic	false
OAI	N	ASN- 28	2.91	141.67	H-Bond (Protein Donor)	false
OAE	ND2	ASN- 28	3.29	141.68	H-Bond (Protein Donor)	false
OAB	N	GLY- 29	2.66	156.3	H-Bond (Protein Donor)	false
OAA	NE2	HIS- 43	2.57	176.67	H-Bond (Protein Donor)	false
CBF	CG1	VAL- 50	4.41	0	Hydrophobic	false
CBE	CG1	VAL- 50	4.41	0	Hydrophobic	false
CAR	CB	VAL- 50	3.8	0	Hydrophobic	false
CBB	CG2	VAL- 50	4.43	0	Hydrophobic	false
CAW	CB	ALA- 69	4.49	0	Hydrophobic	false
CAJ	CB	ALA- 69	3.52	0	Hydrophobic	false
CAY	CB	SER- 71	4.3	0	Hydrophobic	false
OAF	OG	SER- 71	2.75	161.3	H-Bond (Protein Donor)	false
CAT	CB	ALA- 92	4.31	0	Hydrophobic	false
CAM	CD2	LEU- 93	4.11	0	Hydrophobic	false
CAL	CB	GLU- 96	3.99	0	Hydrophobic	false
CAL	CD1	LEU- 100	3.71	0	Hydrophobic	false
CAM	CD2	LEU- 107	4.48	0	Hydrophobic	false
CBG	CD1	ILE- 141	4.48	0	Hydrophobic	false
CAT	CG1	ILE- 141	4.49	0	Hydrophobic	false