scPDB - 1v8l entry

Protein Data Bank Entry:

PDB ID : 1v8l

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-01-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-ribose pyrophosphatase
ID:	Q84CU3_THETH
AC:	Q84CU3
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.716
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.027	519.750

% Hydrophobic	% Polar
32.47	67.53
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	30.59 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
6.19089	10.5773	47.7572

Binding mode :

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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
C4D	CB	ALA- 36	4	0	Hydrophobic	false
O1B	NH1	ARG- 54	2.78	160.72	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 54	3.01	157.5	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 54	3.6	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 54	3.74	0	Ionic (Protein Cationic)	false
C4D	CB	ALA- 66	4.43	0	Hydrophobic	false
O2A	N	LEU- 68	2.87	165.95	H-Bond (Protein Donor)	false
C5D	CD1	LEU- 68	3.21	0	Hydrophobic	false
O1D	O	HOH- 627	2.95	132.84	H-Bond (Protein Donor)	false