scPDB - 3juk entry

Protein Data Bank Entry:

PDB ID : 3juk

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-09-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UTP--glucose-1-phosphate uridylyltransferase
ID:	O25363_HELPY
AC:	O25363
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.177
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.176	945.000

% Hydrophobic	% Polar
31.79	68.21
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	70.31 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
59.7455	41.7963	57.278

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
C1C	CB	PRO- 8	3.9	0	Hydrophobic	false
C4C	CB	PRO- 8	4.39	0	Hydrophobic	false
O2	N	ALA- 10	3.01	144.88	H-Bond (Protein Donor)	false
O2C	N	GLY- 11	2.97	137.11	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 25	2.94	0	Ionic (Protein Cationic)	false
O2C	OE2	GLU- 26	3.06	167.43	H-Bond (Ligand Donor)	false
O3C	OE2	GLU- 26	3.01	147.39	H-Bond (Ligand Donor)	false
N3	OE1	GLN- 102	2.74	163.4	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 102	3.36	134.36	H-Bond (Protein Donor)	false
O4	N	GLY- 107	3.02	145.34	H-Bond (Protein Donor)	false
C4C	CD1	LEU- 108	4.22	0	Hydrophobic	false
C5C	CD2	LEU- 108	4.18	0	Hydrophobic	false
C2'	CD2	LEU- 108	4.17	0	Hydrophobic	false
C4C	CG	LEU- 128	3.91	0	Hydrophobic	false
C1'	CD2	LEU- 128	3.97	0	Hydrophobic	false
O6'	OD1	ASP- 131	3.46	130.04	H-Bond (Ligand Donor)	false
C6'	CD2	TYR- 170	3.61	0	Hydrophobic	false
O3'	N	GLY- 171	3.32	120.21	H-Bond (Protein Donor)	false
O4'	N	GLY- 171	3.28	166.72	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 190	2.81	161.7	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 190	2.78	170.7	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 191	2.62	128.54	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 191	2.62	0	Ionic (Protein Cationic)	false
C4'	CB	VAL- 203	4.34	0	Hydrophobic	false
O2'	O	HOH- 291	3.03	141.41	H-Bond (Protein Donor)	false
O2A	MG	MG- 301	2.33	0	Metal Acceptor	false
O1B	MG	MG- 301	2.31	0	Metal Acceptor	false