scPDB - 1nly entry

Protein Data Bank Entry:

PDB ID : 1nly

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2003-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cag alpha
ID:	Q7BK04_HELPX
AC:	Q7BK04
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	210
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.054
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.384	604.125

% Hydrophobic	% Polar
41.90	58.10
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	59.72 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-40.6604	54.5413	21.6779

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'	OD1	ASN- 61	2.67	128.21	H-Bond (Ligand Donor)	false
O3B	NH2	ARG- 133	3.15	157.3	H-Bond (Protein Donor)	false
C5'	CB	SER- 136	4.27	0	Hydrophobic	false
C2'	CE1	TYR- 140	4.49	0	Hydrophobic	false
O2'	OH	TYR- 140	2.78	135.01	H-Bond (Ligand Donor)	false
O3B	N	GLY- 181	2.88	154.66	H-Bond (Protein Donor)	false
O1B	N	GLY- 183	3.31	147.22	H-Bond (Protein Donor)	false
O3A	N	GLY- 183	3.4	150.62	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 184	3	143.32	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 184	2.85	136.55	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 184	3.46	126.72	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 184	3	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 184	2.85	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 184	3.46	0	Ionic (Protein Cationic)	false
O2B	N	THR- 185	3.45	176.26	H-Bond (Protein Donor)	false
O1A	OG1	THR- 186	2.86	158.21	H-Bond (Protein Donor)	false
O1A	N	THR- 186	3.17	171.73	H-Bond (Protein Donor)	false
O2B	MG	MG- 401	2.58	0	Metal Acceptor	false