scPDB - 2gn8 entry

Protein Data Bank Entry:

PDB ID : 2gn8

Resolution :2.100 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
B	100 %

Ligand binding site composition:

B-Factor:	28.046
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.976	1491.750

% Hydrophobic	% Polar
42.76	57.24
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	73.81 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
29.7838	30.9639	5.92556

Binding mode :

What is Poseview ?

2D View
3D View

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
O3B	OG1	THR- 19	2.7	143.69	H-Bond (Protein Donor)	false
O1A	N	SER- 21	3.06	168.14	H-Bond (Protein Donor)	false
O1N	OG	SER- 21	2.91	147.73	H-Bond (Protein Donor)	false
O1N	N	PHE- 22	2.7	169.5	H-Bond (Protein Donor)	false
C5D	CB	PHE- 22	4.08	0	Hydrophobic	false
O2X	CZ	ARG- 44	3.93	0	Ionic (Protein Cationic)	false
O2X	NE	ARG- 44	2.99	164.17	H-Bond (Protein Donor)	false
O2X	N	ARG- 44	2.81	156.46	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 44	3.3	163.64	H-Bond (Protein Donor)	false
O1X	N	ASP- 45	2.68	147.91	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 48	3.29	122.27	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 48	3.29	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 48	3.71	0	Ionic (Protein Cationic)	false
N6A	OD1	ASP- 67	2.94	152.33	H-Bond (Ligand Donor)	false
N1A	N	VAL- 68	2.9	163.8	H-Bond (Protein Donor)	false
C5D	CB	ALA- 87	4.09	0	Hydrophobic	false
C1B	CB	ALA- 88	4.35	0	Hydrophobic	false
C3D	CB	ALA- 89	3.84	0	Hydrophobic	false
O2N	NZ	LYS- 91	2.69	158.52	H-Bond (Protein Donor)	false
O7N	NZ	LYS- 91	2.7	140.24	H-Bond (Protein Donor)	false
O2N	NZ	LYS- 91	2.69	0	Ionic (Protein Cationic)	false
N6A	OG1	THR- 106	3.39	124.64	H-Bond (Ligand Donor)	false
C4D	CD1	LEU- 129	3.63	0	Hydrophobic	false
C5N	CB	THR- 131	4.11	0	Hydrophobic	false
O2D	OH	TYR- 141	2.69	147.16	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 145	2.84	157.86	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 145	2.9	124.17	H-Bond (Protein Donor)	false
C4N	CG2	VAL- 174	4.07	0	Hydrophobic	false
O1A	CZ	ARG- 178	3.25	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 178	3.82	0	Ionic (Protein Cationic)	false