scPDB - 4xsr entry

Protein Data Bank Entry:

PDB ID : 4xsr

Resolution :2.390 Å

Experimental Method : X-ray

Deposition Date : 2015-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alr3699 protein
ID:	Q8YQW3_NOSS1
AC:	Q8YQW3
Organism:	Nostoc sp.
Reign:	Bacteria
TaxID:	103690
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	45.960
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.986	1356.750

% Hydrophobic	% Polar
45.52	54.48
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	72.99 %
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
38.3524	-68.5511	17.3007

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
O2B	N	GLY- 14	2.78	156.13	H-Bond (Protein Donor)	false
C1C	CD1	LEU- 17	3.71	0	Hydrophobic	false
C4C	CD1	LEU- 17	3.78	0	Hydrophobic	false
C6'	CB	CYS- 18	4.42	0	Hydrophobic	false
C1'	CB	HIS- 121	4.27	0	Hydrophobic	false
O6'	ND1	HIS- 121	2.82	155.2	H-Bond (Ligand Donor)	false
O6'	ND2	ASN- 151	2.85	165.77	H-Bond (Protein Donor)	false
O6'	ND2	ASN- 174	3.39	147.95	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 213	2.77	140.09	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 213	2.77	149.94	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 213	2.77	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 213	2.77	0	Ionic (Protein Cationic)	false
N3	O	ARG- 267	2.74	155.98	H-Bond (Ligand Donor)	false
O4	N	ARG- 267	2.9	167.12	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 288	2.58	146.67	H-Bond (Ligand Donor)	false
C2'	CG	PRO- 289	4	0	Hydrophobic	false
C3'	CB	PRO- 289	4.33	0	Hydrophobic	false
C4'	CB	PHE- 290	3.73	0	Hydrophobic	false
O3'	N	PHE- 290	2.94	162.5	H-Bond (Protein Donor)	false
O3'	N	GLY- 291	3.45	133.68	H-Bond (Protein Donor)	false
O4'	N	GLY- 291	3.02	153.12	H-Bond (Protein Donor)	false
C3C	CB	ARG- 292	3.72	0	Hydrophobic	false
C4C	CD	ARG- 292	4.25	0	Hydrophobic	false
C6'	CD	ARG- 292	4	0	Hydrophobic	false
O3C	NE	ARG- 292	2.93	155.02	H-Bond (Protein Donor)	false
O1A	N	ARG- 292	2.89	167.51	H-Bond (Protein Donor)	false
C5C	CG1	VAL- 293	4.23	0	Hydrophobic	false
C3C	CG1	VAL- 293	4.07	0	Hydrophobic	false
O2C	OE1	GLU- 296	3.06	134.81	H-Bond (Ligand Donor)	false
O3C	OE1	GLU- 296	2.61	149.34	H-Bond (Ligand Donor)	false
O3C	OE2	GLU- 296	3.42	124.71	H-Bond (Ligand Donor)	false
O2A	O	HOH- 523	2.65	133.97	H-Bond (Protein Donor)	false