scPDB - 4ri1 entry

Protein Data Bank Entry:

PDB ID : 4ri1

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2014-10-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
ID:	PSEH_HELPY
AC:	O25094
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	2.3.1.202

Chains:

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

Ligand binding site composition:

B-Factor:	44.182
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.263	1093.500

% Hydrophobic	% Polar
54.32	45.68
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	42.47 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-28.8564	2.50459	-22.5694

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
CEP	CG2	ILE- 93	3.68	0	Hydrophobic	false
N4P	O	ILE- 93	2.72	165.91	H-Bond (Ligand Donor)	false
O	N	ILE- 93	3.05	153.74	H-Bond (Protein Donor)	false
C6P	CB	TYR- 94	3.74	0	Hydrophobic	false
CAP	CG	LYS- 95	3.95	0	Hydrophobic	false
O9P	N	LYS- 95	2.92	166.05	H-Bond (Protein Donor)	false
O4A	N	GLY- 103	2.92	147.3	H-Bond (Protein Donor)	false
CH3	CB	LEU- 125	3.86	0	Hydrophobic	false
S1P	CG2	VAL- 127	4.19	0	Hydrophobic	false
CH3	CG2	VAL- 127	4.09	0	Hydrophobic	false
O5P	ND2	ASN- 131	3.1	168.68	H-Bond (Protein Donor)	false
N3A	NZ	LYS- 133	3.42	135.56	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 133	2.74	158.21	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 133	2.74	0	Ionic (Protein Cationic)	false
O5A	NZ	LYS- 133	3.47	0	Ionic (Protein Cationic)	false
DuAr	NZ	LYS- 133	3.26	6.06	Pi/Cation	false
CDP	CB	ALA- 134	4.01	0	Hydrophobic	false
CCP	CG	PHE- 137	3.57	0	Hydrophobic	false
CEP	CE2	PHE- 137	4.31	0	Hydrophobic	false
O	OH	TYR- 138	2.92	142.22	H-Bond (Protein Donor)	false
CH3	CE2	TYR- 138	3.84	0	Hydrophobic	false
O2A	NZ	LYS- 140	3.85	0	Ionic (Protein Cationic)	false
O3A	O	HOH- 1410	3.14	179.97	H-Bond (Protein Donor)	false