scPDB - 2h39 entry

Protein Data Bank Entry:

PDB ID : 2h39

Resolution :2.230 Å

Experimental Method : X-ray

Deposition Date : 2006-05-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-glucose phosphorylase
ID:	AGLUP_ARATH
AC:	Q9FK51
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	30 %
B	70 %

Ligand binding site composition:

B-Factor:	16.705
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.067	1123.875

% Hydrophobic	% Polar
40.84	59.16
According to VolSite

Ligand :

HET Code:	ADQ
Formula:	C16H23N5O15P2
Molecular weight:	587.326 g/mol
DrugBank ID:	DB01774
Buried Surface Area:	75.01 %
Polar Surface area:	337.03 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	7
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
32.7824	-3.30584	-24.6862

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
O1B	NH1	ARG- 41	3.38	157.67	H-Bond (Protein Donor)	false
O3D	NH2	ARG- 41	2.62	163.11	H-Bond (Protein Donor)	false
O2B	NE	ARG- 44	2.92	154.72	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 44	3.35	128.3	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 44	3.84	0	Ionic (Protein Cationic)	false
C3D	CD	ARG- 44	4.37	0	Hydrophobic	false
C2D	CB	ARG- 44	4.29	0	Hydrophobic	false
C1D	CZ	PHE- 65	4.34	0	Hydrophobic	false
N6	O	GLU- 72	3	143.91	H-Bond (Ligand Donor)	false
N1	N	ALA- 74	3.33	165.63	H-Bond (Protein Donor)	false
O3D	ND2	ASN- 94	3.02	159.68	H-Bond (Protein Donor)	false
O2D	OD1	ASN- 94	2.59	159.25	H-Bond (Ligand Donor)	false
N3	N	LEU- 95	3.28	164.79	H-Bond (Protein Donor)	false
C2D	CD1	TYR- 96	4.19	0	Hydrophobic	false
C4D	CG2	VAL- 126	4.22	0	Hydrophobic	false
C1D	CG2	VAL- 126	4.23	0	Hydrophobic	false
C6'	CZ	PHE- 171	3.71	0	Hydrophobic	false
O2A	ND2	ASN- 173	2.92	149.91	H-Bond (Protein Donor)	false
O3A	ND2	ASN- 173	3.26	141.54	H-Bond (Protein Donor)	false
O2'	O	GLY- 179	2.56	163.73	H-Bond (Ligand Donor)	false
O2B	OG	SER- 181	2.71	162.03	H-Bond (Protein Donor)	false
O1A	N	SER- 181	2.68	158.69	H-Bond (Protein Donor)	false
O1A	N	MET- 182	3.13	168.56	H-Bond (Protein Donor)	false
C5D	CG	MET- 182	3.73	0	Hydrophobic	false
O1B	NE2	GLN- 188	2.71	143.28	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 188	3.17	128.46	H-Bond (Protein Donor)	false
C6'	CB	PHE- 325	3.8	0	Hydrophobic	false
O6'	N	PHE- 325	3.07	155.86	H-Bond (Protein Donor)	false
O4'	OE2	GLU- 326	3.41	137.65	H-Bond (Ligand Donor)	false
O4'	OE1	GLU- 326	2.55	164.6	H-Bond (Ligand Donor)	false
O6'	OE2	GLU- 326	2.71	141.06	H-Bond (Ligand Donor)	false
O2A	O	HOH- 537	2.67	179.98	H-Bond (Protein Donor)	false