scPDB - 4b2g entry

Protein Data Bank Entry:

PDB ID : 4b2g

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2012-07-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	F6H697_VITVI
AC:	F6H697
Organism:	Vitis vinifera
Reign:	Eukaryota
TaxID:	29760
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.861
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.930	1623.375

% Hydrophobic	% Polar
49.06	50.94
According to VolSite

Ligand :

HET Code:	V1N
Formula:	C19H20N6O7P
Molecular weight:	475.372 g/mol
DrugBank ID:	-
Buried Surface Area:	72.78 %
Polar Surface area:	203.49 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-25.2041	24.7037	1.74082

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
O16	OG	SER- 108	2.51	165.23	H-Bond (Protein Donor)	false
O16	N	SER- 108	3.11	155.1	H-Bond (Protein Donor)	false
C24	CD2	LEU- 173	4.14	0	Hydrophobic	false
C26	CG1	VAL- 229	4.05	0	Hydrophobic	false
C20	CZ	PHE- 230	3.63	0	Hydrophobic	false
C26	CD1	ILE- 310	3.8	0	Hydrophobic	false
N3	OG1	THR- 312	2.87	150.27	H-Bond (Protein Donor)	false
N1	O	MET- 335	2.98	143.97	H-Bond (Ligand Donor)	false
C28	CB	MET- 335	3.88	0	Hydrophobic	false
C24	CB	ALA- 337	3.68	0	Hydrophobic	false
C13	CB	SER- 338	4.16	0	Hydrophobic	false
O17	N	SER- 339	2.71	172.61	H-Bond (Protein Donor)	false
N23	OH	TYR- 342	3.08	148.61	H-Bond (Ligand Donor)	false
N1	OH	TYR- 358	3.06	164.38	H-Bond (Ligand Donor)	false
O33	OD1	ASP- 416	2.83	156.07	H-Bond (Ligand Donor)	false
O31	OD2	ASP- 416	3.1	156.08	H-Bond (Ligand Donor)	false
C32	CE2	PHE- 432	4.22	0	Hydrophobic	false