scPDB - 3qvt entry

Protein Data Bank Entry:

PDB ID : 3qvt

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-02-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Myo-inositol-1-phosphate synthase (Ino1)
ID:	O28480_ARCFU
AC:	O28480
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.990
Number of residues:	59
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.315	600.750

% Hydrophobic	% Polar
43.82	56.18
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	81.52 %
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
11.7671	26.2816	19.335

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
O1A	N	ILE- 11	3.1	153.06	H-Bond (Protein Donor)	false
O2N	N	VAL- 12	2.96	172.56	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 12	4.3	0	Hydrophobic	false
O3B	OE1	GLU- 57	2.55	174.69	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 57	2.72	169.87	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 57	3.41	127.17	H-Bond (Ligand Donor)	false
O3B	NE	ARG- 59	3.18	140.13	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 59	2.88	154.26	H-Bond (Protein Donor)	false
O2B	NE	ARG- 59	3.14	139.25	H-Bond (Protein Donor)	false
N6A	O	THR- 99	2.86	139.36	H-Bond (Ligand Donor)	false
C2B	CD1	LEU- 110	3.8	0	Hydrophobic	false
C5D	CB	VAL- 147	4.49	0	Hydrophobic	false
O3D	O	ALA- 148	2.71	153.41	H-Bond (Ligand Donor)	false
O3D	OG1	THR- 150	3.05	156.81	H-Bond (Protein Donor)	false
N1A	OH	TYR- 185	2.91	130.3	H-Bond (Protein Donor)	false
C4N	CE1	PHE- 199	4.36	0	Hydrophobic	false
C4D	CG2	THR- 200	4.15	0	Hydrophobic	false
C1D	CG2	THR- 200	4.41	0	Hydrophobic	false
N7N	OG1	THR- 228	2.97	150.92	H-Bond (Ligand Donor)	false
C4N	CG2	THR- 228	3.89	0	Hydrophobic	false
O2D	OD2	ASP- 261	3.14	138.72	H-Bond (Ligand Donor)	false
N7N	O	ASP- 332	3.32	138.11	H-Bond (Ligand Donor)	false