scPDB - 3c4v entry

Protein Data Bank Entry:

PDB ID : 3c4v

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2008-01-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-inositol 3-phosphate glycosyltransferase
ID:	MSHA_CORGL
AC:	Q8NTA6
Organism:	Corynebacterium glutamicum
Reign:	Bacteria
TaxID:	196627
EC Number:	2.4.1.250

Chains:

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

Ligand binding site composition:

B-Factor:	44.939
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.098	685.125

% Hydrophobic	% Polar
39.90	60.10
According to VolSite

Ligand :

HET Code:	LIP
Formula:	C6H11O9P
Molecular weight:	258.120 g/mol
DrugBank ID:	DB03542
Buried Surface Area:	70.44 %
Polar Surface area:	183.38 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
99.4119	42.7576	-10.9718

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
O5	NE2	HIS- 9	2.71	134.62	H-Bond (Protein Donor)	false
O4	O	ASP- 20	3.27	167.97	H-Bond (Ligand Donor)	false
O5	O	ASP- 20	2.68	154.69	H-Bond (Ligand Donor)	false
O3	N	MET- 24	3.1	157.64	H-Bond (Protein Donor)	false
C4	CB	MET- 24	3.64	0	Hydrophobic	false
O8	NZ	LYS- 78	2.54	160.5	H-Bond (Protein Donor)	false
O8	NZ	LYS- 78	2.54	0	Ionic (Protein Cationic)	false
O9	NZ	LYS- 78	3.74	0	Ionic (Protein Cationic)	false
C6	CE1	TYR- 110	4.36	0	Hydrophobic	false
O8	OH	TYR- 110	2.71	122	H-Bond (Protein Donor)	false
C2	CG2	THR- 134	4.34	0	Hydrophobic	false
O7	OG1	THR- 134	2.96	174.27	H-Bond (Protein Donor)	false
O7	CZ	ARG- 154	3.9	0	Ionic (Protein Cationic)	false
O7	NH2	ARG- 154	3.24	165.5	H-Bond (Protein Donor)	false