scPDB - 3imx entry

Protein Data Bank Entry:

PDB ID : 3imx

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-08-11

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:	22.482
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.566	823.500

% Hydrophobic	% Polar
63.11	36.89
According to VolSite

Ligand :

HET Code:	B84
Formula:	C26H34N5O4S2
Molecular weight:	544.709 g/mol
DrugBank ID:	-
Buried Surface Area:	68.04 %
Polar Surface area:	142.54 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-0.103135	2.48208	-16.3409

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
C34	CG1	VAL- 62	3.68	0	Hydrophobic	false
C39	CG1	VAL- 62	4.46	0	Hydrophobic	false
N53	O	ARG- 63	2.73	149.3	H-Bond (Ligand Donor)	false
C62	CD	ARG- 63	4.31	0	Hydrophobic	false
N65	N	ARG- 63	3.11	165.01	H-Bond (Protein Donor)	false
C45	CB	SER- 64	3.95	0	Hydrophobic	false
S56	CG	PRO- 66	4.15	0	Hydrophobic	false
N11	OG	SER- 69	2.83	153.81	H-Bond (Ligand Donor)	false
C15	CB	SER- 69	4.03	0	Hydrophobic	false
S56	CD1	ILE- 159	3.95	0	Hydrophobic	false
C60	CG2	ILE- 159	4.37	0	Hydrophobic	false
C62	CD1	ILE- 159	4.34	0	Hydrophobic	false
C39	CE	MET- 210	3.89	0	Hydrophobic	false
C39	CG1	ILE- 211	4.4	0	Hydrophobic	false
C30	CG2	ILE- 211	3.61	0	Hydrophobic	false
C37	CE2	TYR- 214	4.06	0	Hydrophobic	false
C42	CD1	TYR- 214	3.75	0	Hydrophobic	false
C45	CE1	TYR- 214	3.93	0	Hydrophobic	false
C48	CZ	TYR- 214	3.79	0	Hydrophobic	false
C23	CE2	TYR- 214	3.48	0	Hydrophobic	false
C5	CD1	TYR- 215	4.42	0	Hydrophobic	false
C45	CE	MET- 235	3.56	0	Hydrophobic	false
C5	CD2	LEU- 451	3.82	0	Hydrophobic	false
S56	CG2	VAL- 452	4.13	0	Hydrophobic	false
C5	CG2	VAL- 455	4.07	0	Hydrophobic	false
C15	CG2	VAL- 455	4.44	0	Hydrophobic	false
S56	CG1	VAL- 455	3.83	0	Hydrophobic	false
C30	CG2	VAL- 455	3.93	0	Hydrophobic	false
S56	CB	ALA- 456	4.24	0	Hydrophobic	false
C67	CB	ALA- 456	3.82	0	Hydrophobic	false
C67	CD	LYS- 459	3.99	0	Hydrophobic	false
C60	CD	LYS- 459	3.81	0	Hydrophobic	false