scPDB - 3sgv entry

Protein Data Bank Entry:

PDB ID : 3sgv

Resolution :1.610 Å

Experimental Method : X-ray

Deposition Date : 2011-06-15

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:	23.901
Number of residues:	37
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.452	1269.000

% Hydrophobic	% Polar
62.50	37.50
According to VolSite

Ligand :

HET Code:	2BJ
Formula:	C22H17N2O6
Molecular weight:	405.380 g/mol
DrugBank ID:	-
Buried Surface Area:	62.32 %
Polar Surface area:	124.28 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
22.3231	-1.46883	24.4079

Binding mode :

What is Poseview ?

2D View
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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
N2	O	MET- 25	2.75	161.85	H-Bond (Ligand Donor)	false
C10	CB	MET- 25	3.67	0	Hydrophobic	false
C11	CE	MET- 25	3.81	0	Hydrophobic	false
C6	CB	ASP- 26	4.3	0	Hydrophobic	false
C4	CB	ASP- 26	3.8	0	Hydrophobic	false
O3	N	GLY- 27	3.3	147.01	H-Bond (Protein Donor)	false
O3	N	GLY- 29	2.89	168.04	H-Bond (Protein Donor)	false
O4	NH2	ARG- 39	2.89	146.22	H-Bond (Protein Donor)	false
O4	NH1	ARG- 39	2.89	146.56	H-Bond (Protein Donor)	false
C16	CB	HIS- 43	3.71	0	Hydrophobic	false
C17	CB	ALA- 47	3.83	0	Hydrophobic	false
C11	CG2	VAL- 50	4.14	0	Hydrophobic	false
C12	CB	ALA- 69	3.66	0	Hydrophobic	false
C3	CB	SER- 71	3.67	0	Hydrophobic	false
O4	OE1	GLU- 73	2.65	160.74	H-Bond (Ligand Donor)	false
O5	ND2	ASN- 74	2.69	124.96	H-Bond (Protein Donor)	false
C21	CD1	PHE- 89	3.82	0	Hydrophobic	false
C19	CB	ALA- 92	3.98	0	Hydrophobic	false
C21	CB	ALA- 92	4.02	0	Hydrophobic	false
O1	CZ	ARG- 194	3.86	0	Ionic (Protein Cationic)	false