scPDB - 2gna entry

Protein Data Bank Entry:

PDB ID : 2gna

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2006-04-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
ID:	PSEB_HELPY
AC:	O25511
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	4.2.1.115

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	55.122
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.136	1063.125

% Hydrophobic	% Polar
43.49	56.51
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	59.54 %
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
36.7736	56.5956	-0.479

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
O3'	NZ	LYS- 91	3.1	135.18	H-Bond (Protein Donor)	false
O2'	OG	SER- 177	2.93	139.59	H-Bond (Protein Donor)	false
O3'	O	ARG- 178	3.19	171.46	H-Bond (Ligand Donor)	false
C2'	CB	SER- 180	4.23	0	Hydrophobic	false
C5D	CB	VAL- 181	4.21	0	Hydrophobic	false
O1B	N	VAL- 181	3.12	170.87	H-Bond (Protein Donor)	false
N3	O	PRO- 197	2.8	148.51	H-Bond (Ligand Donor)	false
O2	N	THR- 199	3.34	158.3	H-Bond (Protein Donor)	false
O2D	OG1	THR- 199	2.6	149.22	H-Bond (Protein Donor)	false
C2D	CG2	THR- 199	4.48	0	Hydrophobic	false
C3D	CG	MET- 203	4.41	0	Hydrophobic	false
C4D	CG	ARG- 205	4.31	0	Hydrophobic	false
C1D	CE	MET- 239	3.57	0	Hydrophobic	false
C4D	CE	MET- 239	3.87	0	Hydrophobic	false
O2D	OE2	GLU- 261	3.07	137.31	H-Bond (Ligand Donor)	false
O1A	O	HOH- 408	2.95	160.14	H-Bond (Protein Donor)	false