scPDB - 1xng entry

Protein Data Bank Entry:

PDB ID : 1xng

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2004-10-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NH(3)-dependent NAD(+) synthetase
ID:	NADE_HELPY
AC:	O25096
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	6.3.1.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	34 %
B	66 %

Ligand binding site composition:

B-Factor:	21.415
Number of residues:	52
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:	ATP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.574	617.625

% Hydrophobic	% Polar
57.92	42.08
According to VolSite

Ligand :

HET Code:	DND
Formula:	C21H24N6O15P2
Molecular weight:	662.394 g/mol
DrugBank ID:	DB04099
Buried Surface Area:	63.52 %
Polar Surface area:	340.58 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-24.6671	21.8161	0.238114

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
N1A	NE	ARG- 23	3.27	130.64	H-Bond (Protein Donor)	false
C5D	CG2	THR- 104	4.31	0	Hydrophobic	false
C3D	CG2	THR- 104	4.41	0	Hydrophobic	false
O3P	ND2	ASN- 108	3.26	129.25	H-Bond (Protein Donor)	false
O5D	ND2	ASN- 108	3.49	155.26	H-Bond (Protein Donor)	false
C5N	CB	ALA- 111	4.45	0	Hydrophobic	false
O13	CZ	ARG- 112	3.74	0	Ionic (Protein Cationic)	false
O13	NH2	ARG- 112	2.79	144	H-Bond (Protein Donor)	false
C4B	CD2	TYR- 119	4.07	0	Hydrophobic	false
C1B	CE2	TYR- 119	4.04	0	Hydrophobic	false
O3B	OG	SER- 122	2.87	153.9	H-Bond (Ligand Donor)	false
O2B	OG	SER- 122	2.65	146.11	H-Bond (Ligand Donor)	false
C2B	CD2	LEU- 128	4.23	0	Hydrophobic	false
C2D	CE1	TYR- 142	3.94	0	Hydrophobic	false
C5N	CB	THR- 144	4.04	0	Hydrophobic	false
O14	N	LEU- 145	2.94	168.97	H-Bond (Protein Donor)	false
C3N	CB	ALA- 184	3.63	0	Hydrophobic	false
C5N	CD1	LEU- 186	3.52	0	Hydrophobic	false
O2D	NE2	GLN- 190	3.4	121.04	H-Bond (Protein Donor)	false
C1B	CE1	PHE- 246	3.93	0	Hydrophobic	false
C5B	CZ	PHE- 246	4.31	0	Hydrophobic	false
DuAr	DuAr	PHE- 246	3.58	0	Aromatic Face/Face	false
O12	NZ	LYS- 247	2.71	172.58	H-Bond (Protein Donor)	false
O12	NZ	LYS- 247	2.71	0	Ionic (Protein Cationic)	false
O14	NZ	LYS- 247	3.1	0	Ionic (Protein Cationic)	false
O2B	O	HOH- 319	2.69	179.98	H-Bond (Protein Donor)	false
O7N	O	HOH- 343	2.76	179.97	H-Bond (Protein Donor)	false