scPDB - 4l8v entry

Protein Data Bank Entry:

PDB ID : 4l8v

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2013-06-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
ID:	IOLG_BACSU
AC:	P26935
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	1.1.1.18

Chains:

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

Ligand binding site composition:

B-Factor:	51.661
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.766	749.250

% Hydrophobic	% Polar
41.89	58.11
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	45.4 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
32.4851	64.1371	6.84927

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
O2A	N	LYS- 12	3.1	159.66	H-Bond (Protein Donor)	false
O2N	N	ILE- 13	3.17	174.92	H-Bond (Protein Donor)	false
C5D	CG2	ILE- 13	3.75	0	Hydrophobic	false
C4N	CD1	ILE- 13	4.32	0	Hydrophobic	false
O3B	OG	SER- 35	3.38	166.76	H-Bond (Protein Donor)	false
O4B	N	TRP- 75	2.94	120.75	H-Bond (Protein Donor)	false
C1B	CB	TRP- 75	4.12	0	Hydrophobic	false
C4D	CB	GLU- 96	4.44	0	Hydrophobic	false
N7N	OE1	GLU- 96	2.8	164.05	H-Bond (Ligand Donor)	false
O3D	O	LYS- 97	2.59	161.2	H-Bond (Ligand Donor)	false
O2D	O	LYS- 97	3	164.21	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 97	2.99	124.77	H-Bond (Protein Donor)	false