scPDB - 3vf6 entry

Protein Data Bank Entry:

PDB ID : 3vf6

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2012-01-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucokinase
ID:	HXK4_HUMAN
AC:	P35557
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	31.526
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.485	516.375

% Hydrophobic	% Polar
64.05	35.95
According to VolSite

Ligand :

HET Code:	0H6
Formula:	C18H18F3N4O3
Molecular weight:	395.356 g/mol
DrugBank ID:	DB11765
Buried Surface Area:	60.04 %
Polar Surface area:	99.94 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-8.89529	1.6085	20.7124

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
C4	CG1	VAL- 62	3.67	0	Hydrophobic	false
N10	O	ARG- 63	2.8	175.48	H-Bond (Ligand Donor)	false
N17	N	ARG- 63	2.85	169.37	H-Bond (Protein Donor)	false
C14	CD1	ILE- 159	4.07	0	Hydrophobic	false
C9	CE	MET- 210	3.58	0	Hydrophobic	false
C4	CG1	ILE- 211	4.24	0	Hydrophobic	false
C9	CG1	ILE- 211	4.07	0	Hydrophobic	false
F26	CG2	ILE- 211	3.64	0	Hydrophobic	false
C7	CE1	TYR- 214	3.78	0	Hydrophobic	false
C6	CZ	TYR- 214	4.3	0	Hydrophobic	false
C9	CG	TYR- 214	4.11	0	Hydrophobic	false
C8	CD1	TYR- 214	3.71	0	Hydrophobic	false
C5	CD2	TYR- 214	3.98	0	Hydrophobic	false
F28	CD2	TYR- 214	3.77	0	Hydrophobic	false
F28	CD1	TYR- 215	3.5	0	Hydrophobic	false
C6	CE	MET- 235	4.19	0	Hydrophobic	false
C8	SD	MET- 235	3.84	0	Hydrophobic	false
F26	CB	LEU- 451	3.8	0	Hydrophobic	false
F27	CD2	LEU- 451	4.43	0	Hydrophobic	false
C13	CG2	VAL- 452	3.81	0	Hydrophobic	false
C13	CG1	VAL- 455	3.52	0	Hydrophobic	false
F27	CG2	VAL- 455	3.79	0	Hydrophobic	false
C14	CB	ALA- 456	4.07	0	Hydrophobic	false
O19	O	HOH- 656	2.69	171.63	H-Bond (Protein Donor)	false