scPDB - 3qvx entry

Protein Data Bank Entry:

PDB ID : 3qvx

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-02-26

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:	18.101
Number of residues:	59
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.772	654.750

% Hydrophobic	% Polar
48.97	51.03
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	81.12 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
11.7132	26.1517	19.2262

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
O2A	N	ILE- 11	3.08	170.81	H-Bond (Protein Donor)	false
O2N	N	VAL- 12	2.93	172.33	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 12	4.3	0	Hydrophobic	false
O3B	OE1	GLU- 57	2.72	169.19	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 57	2.99	165.13	H-Bond (Ligand Donor)	false
O3B	NE	ARG- 59	3.21	149.02	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 59	3.11	151.2	H-Bond (Protein Donor)	false
O2B	NE	ARG- 59	3.14	135.95	H-Bond (Protein Donor)	false
C2B	CG	ARG- 59	4.48	0	Hydrophobic	false
N6A	O	THR- 99	2.75	136.4	H-Bond (Ligand Donor)	false
C2B	CD1	LEU- 110	3.78	0	Hydrophobic	false
O3D	O	ALA- 148	2.72	168.53	H-Bond (Ligand Donor)	false
O4B	N	SER- 149	3.47	134.52	H-Bond (Protein Donor)	false
O3D	OG1	THR- 150	3.04	164.65	H-Bond (Protein Donor)	false
N1A	OH	TYR- 185	2.75	140.27	H-Bond (Protein Donor)	false
C4D	CG2	THR- 200	4.08	0	Hydrophobic	false
N7N	OG1	THR- 228	2.89	161.2	H-Bond (Ligand Donor)	false
C4N	CG2	THR- 228	3.94	0	Hydrophobic	false
O2D	OD2	ASP- 261	2.72	154.3	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 274	3.35	123.84	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 274	4	128.27	Pi/Cation	false
N7N	O	ASP- 332	3.02	141.63	H-Bond (Ligand Donor)	false
C3N	CB	ALA- 336	4.4	0	Hydrophobic	false
O2N	O	HOH- 421	2.86	156.74	H-Bond (Protein Donor)	false