scPDB - 5bwm entry

Protein Data Bank Entry:

PDB ID : 5bwm

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-06-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-ribosyltransferase
ID:	Q8KNY0_BACCE
AC:	Q8KNY0
Organism:	Bacillus cereus
Reign:	Bacteria
TaxID:	1396
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	71.665
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.274	958.500

% Hydrophobic	% Polar
37.32	62.68
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	66.09 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-15.999	17.6654	13.5735

Binding mode :

What is Poseview ?

2D View
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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
O3D	OD1	ASN- 41	3.2	165.06	H-Bond (Ligand Donor)	false
C3D	CE2	TYR- 47	4.21	0	Hydrophobic	false
C3D	CB	ALA- 51	3.69	0	Hydrophobic	false
O1A	ND2	ASN- 55	2.88	161.63	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 97	3.4	0	Ionic (Protein Cationic)	false
O7N	N	GLY- 98	3.31	149.65	H-Bond (Protein Donor)	false
N7N	O	GLY- 98	3.29	160.63	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 99	3.08	148.65	H-Bond (Ligand Donor)	false
O2B	N	ASP- 100	2.98	165.98	H-Bond (Protein Donor)	false
O3B	NE1	TRP- 102	3.4	121.3	H-Bond (Protein Donor)	false
C4N	CB	SER- 142	4.36	0	Hydrophobic	false
C2D	CB	SER- 142	3.48	0	Hydrophobic	false
C4N	CB	SER- 144	4.32	0	Hydrophobic	false
C1D	CE2	TYR- 151	4.15	0	Hydrophobic	false
O7N	N	TYR- 151	2.69	154.81	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 155	2.63	171.98	H-Bond (Protein Donor)	false
O2N	NH2	ARG- 155	3.36	159.97	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 155	3.53	0	Ionic (Protein Cationic)	false
O2D	OE2	GLU- 185	3.37	128.53	H-Bond (Ligand Donor)	false
O2D	OE1	GLU- 185	2.83	170.24	H-Bond (Ligand Donor)	false