scPDB - 2gn9 entry

Protein Data Bank Entry:

PDB ID : 2gn9

Resolution :2.800 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	98 %
B	2 %

Ligand binding site composition:

B-Factor:	60.623
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.281	1049.625

% Hydrophobic	% Polar
59.16	40.84
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	66.26 %
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
10.6213	29.4526	5.045

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
C3'	CD	LYS- 91	4.23	0	Hydrophobic	false
C4'	CB	LYS- 91	3.91	0	Hydrophobic	false
O4'	O	LYS- 91	2.77	174.52	H-Bond (Ligand Donor)	false
O6'	OG1	THR- 131	2.76	165.2	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 133	2.7	160.82	H-Bond (Protein Donor)	false
O6'	NZ	LYS- 133	3.16	142.51	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 133	2.7	0	Ionic (Protein Cationic)	false
C6'	CD	LYS- 133	4.09	0	Hydrophobic	false
C6'	CE2	TYR- 141	4.49	0	Hydrophobic	false
O6'	OH	TYR- 141	3.3	138.68	H-Bond (Ligand Donor)	false
O2B	ND2	ASN- 173	3.42	127.02	H-Bond (Protein Donor)	false
C5C	CG2	VAL- 181	4.3	0	Hydrophobic	false
C2C	CG2	THR- 199	4.32	0	Hydrophobic	false
O2C	OG1	THR- 199	2.69	153.17	H-Bond (Protein Donor)	false
C3C	CG	MET- 203	4.24	0	Hydrophobic	false
O2B	NE	ARG- 205	2.97	170.82	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 205	3.87	0	Ionic (Protein Cationic)	false
C3C	CG	ARG- 205	4.46	0	Hydrophobic	false
C1C	CE	MET- 239	3.51	0	Hydrophobic	false
C4C	SD	MET- 239	3.55	0	Hydrophobic	false
O1A	CZ	ARG- 258	3.18	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 258	3.92	0	Ionic (Protein Cationic)	false
O2C	OE2	GLU- 261	2.67	164.06	H-Bond (Ligand Donor)	false
C6'	C4N	NAP- 334	3.91	0	Hydrophobic	false