scPDB - 3vgl entry

Protein Data Bank Entry:

PDB ID : 3vgl

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2011-08-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucokinase
ID:	B1VZT1_STRGG
AC:	B1VZT1
Organism:	Streptomyces griseus subsp. griseus
Reign:	Bacteria
TaxID:	455632
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.869
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.614	752.625

% Hydrophobic	% Polar
47.53	52.47
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	64.41 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
13.9613	24.8128	13.8354

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
O2B	N	THR- 12	2.78	149.34	H-Bond (Protein Donor)	false
C5'	CB	THR- 12	4.4	0	Hydrophobic	false
O2B	N	LYS- 13	2.78	153.55	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 13	2.55	154.75	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 13	2.55	0	Ionic (Protein Cationic)	false
O1B	OG1	THR- 132	2.72	157.8	H-Bond (Protein Donor)	false
O1B	N	THR- 132	2.89	164.01	H-Bond (Protein Donor)	false
O2'	N	GLY- 215	3.41	122.6	H-Bond (Protein Donor)	false
N1	OG	SER- 219	2.64	147.94	H-Bond (Protein Donor)	false
O2A	N	GLY- 261	2.94	157.67	H-Bond (Protein Donor)	false
N6	OE2	GLU- 265	2.74	166.72	H-Bond (Ligand Donor)	false
N3B	O	HOH- 359	2.97	147.76	H-Bond (Ligand Donor)	false