scPDB - 3bos entry

Protein Data Bank Entry:

PDB ID : 3bos

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2007-12-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Regulatory inactivation of DnaA Hda protein
ID:	A1S6W5_SHEAM
AC:	A1S6W5
Organism:	Shewanella amazonensis
Reign:	Bacteria
TaxID:	326297
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	18.015
Number of residues:	41
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.427	675.000

% Hydrophobic	% Polar
40.50	59.50
According to VolSite

Ligand :

HET Code:	CDP
Formula:	C9H12N3O11P2
Molecular weight:	400.153 g/mol
DrugBank ID:	DB04555
Buried Surface Area:	77.05 %
Polar Surface area:	249.77 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
36.9855	75.3601	29.0326

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
N3	N	TYR- 30	3.1	154.09	H-Bond (Protein Donor)	false
N4	O	TYR- 30	2.93	160.8	H-Bond (Ligand Donor)	false
O3B	N	LYS- 61	2.85	156.3	H-Bond (Protein Donor)	false
O2B	N	GLY- 63	2.98	156.57	H-Bond (Protein Donor)	false
O3A	N	GLY- 63	3.39	132.08	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 64	3.22	167.14	H-Bond (Protein Donor)	false
O2B	N	ARG- 64	2.9	162.36	H-Bond (Protein Donor)	false
O2B	NE	ARG- 64	2.83	176.33	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 64	3.64	0	Ionic (Protein Cationic)	false
O1B	N	THR- 65	3.06	161.46	H-Bond (Protein Donor)	false
O1A	N	HIS- 66	2.77	161.01	H-Bond (Protein Donor)	false
C2'	CB	HIS- 66	3.87	0	Hydrophobic	false
O2'	ND1	HIS- 66	2.55	163.65	H-Bond (Ligand Donor)	false
O2'	NH2	ARG- 185	2.87	146.75	H-Bond (Protein Donor)	false
O2	NH2	ARG- 185	2.91	138.28	H-Bond (Protein Donor)	false
C4'	CB	LEU- 209	3.97	0	Hydrophobic	false
O2A	NH2	ARG- 210	3.07	147.74	H-Bond (Protein Donor)	false
O2A	NE	ARG- 210	3.05	151.62	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 210	3.5	0	Ionic (Protein Cationic)	false
C3'	CB	ARG- 210	4.03	0	Hydrophobic	false
C1'	CE2	PHE- 213	4.13	0	Hydrophobic	false
O1B	MG	MG- 301	2.06	0	Metal Acceptor	false
O2	O	HOH- 322	2.67	161.26	H-Bond (Protein Donor)	false
O3'	O	HOH- 324	2.71	156	H-Bond (Ligand Donor)	false
N4	O	HOH- 333	3.22	167.66	H-Bond (Ligand Donor)	false