scPDB - 5cb3 entry

Protein Data Bank Entry:

PDB ID : 5cb3

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2015-06-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	O-acetyl-ADP-ribose deacetylase
ID:	YMDB_ECOLI
AC:	P0A8D6
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.330
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.067	465.750

% Hydrophobic	% Polar
58.70	41.30
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	70.09 %
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
52.3487	33.4112	90.5964

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
N6	OD1	ASP- 11	2.92	176.85	H-Bond (Ligand Donor)	false
N1	N	ILE- 12	2.95	175.07	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 25	2.78	167.49	H-Bond (Protein Donor)	false
C3D	CB	ASN- 25	3.76	0	Hydrophobic	false
O1D	N	GLY- 33	2.85	159.22	H-Bond (Protein Donor)	false
O2A	N	VAL- 34	2.84	164.93	H-Bond (Protein Donor)	false
O2D	OD2	ASP- 35	2.63	166.61	H-Bond (Ligand Donor)	false
C2D	CB	ASP- 35	3.82	0	Hydrophobic	false
C4'	CB	ALA- 120	4.15	0	Hydrophobic	false
O1B	N	SER- 122	2.81	138.9	H-Bond (Protein Donor)	false
O3'	OG1	THR- 123	3.11	159.05	H-Bond (Ligand Donor)	false
O2B	N	GLY- 124	2.79	134.25	H-Bond (Protein Donor)	false
O1A	N	VAL- 125	2.82	165.95	H-Bond (Protein Donor)	false
C1D	CG2	VAL- 125	4.43	0	Hydrophobic	false
C4D	CG2	VAL- 125	3.27	0	Hydrophobic	false
O2B	N	TYR- 126	3.11	166.97	H-Bond (Protein Donor)	false
C5D	CZ	TYR- 126	3.72	0	Hydrophobic	false
C3D	CZ	TYR- 126	3.85	0	Hydrophobic	false
C4D	CE1	TYR- 126	3.53	0	Hydrophobic	false
C1'	CB	TYR- 159	3.97	0	Hydrophobic	false
DuAr	DuAr	TYR- 159	3.94	0	Aromatic Face/Face	false
N3	O	HOH- 514	2.93	173.02	H-Bond (Protein Donor)	false
O3'	O	HOH- 522	3	171.3	H-Bond (Protein Donor)	false
O3'	O	HOH- 542	3.09	149.62	H-Bond (Protein Donor)	false
O1B	O	HOH- 561	2.95	149.53	H-Bond (Protein Donor)	false