scPDB - 3wie entry

Protein Data Bank Entry:

PDB ID : 3wie

Resolution :2.330 Å

Experimental Method : X-ray

Deposition Date : 2013-09-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose 1-dehydrogenase
ID:	Q979W2_THEVO
AC:	Q979W2
Organism:	Thermoplasma volcanium
Reign:	Archaea
TaxID:	273116
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
C	96 %

Ligand binding site composition:

B-Factor:	47.580
Number of residues:	53
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.869	1474.875

% Hydrophobic	% Polar
34.32	65.68
According to VolSite

Ligand :

HET Code:	DN4
Formula:	C21H23N6O18P3
Molecular weight:	740.358 g/mol
DrugBank ID:	-
Buried Surface Area:	56.6 %
Polar Surface area:	402.58 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	5
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
4.95358	-16.5641	48.6079

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
O3B	N	SER- 194	2.79	149.83	H-Bond (Protein Donor)	false
O2N	N	GLU- 197	2.66	159.25	H-Bond (Protein Donor)	false
C5D	CB	GLU- 197	3.97	0	Hydrophobic	false
O2B	ND2	ASN- 216	2.89	159.35	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 217	3.12	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 217	2.65	135.53	H-Bond (Protein Donor)	false
O2X	NH1	ARG- 217	2.78	130.7	H-Bond (Protein Donor)	false
O2X	NE2	HIS- 218	3.04	139.21	H-Bond (Protein Donor)	false
N6A	OH	TYR- 238	3.01	123.11	H-Bond (Ligand Donor)	false
C5D	CB	THR- 252	3.9	0	Hydrophobic	false
N6A	OG1	THR- 258	3.01	125.54	H-Bond (Ligand Donor)	false
C4D	CD2	PHE- 275	4.43	0	Hydrophobic	false
C3N	CZ	PHE- 275	3.44	0	Hydrophobic	false
O3D	O	PHE- 277	3.05	120.47	H-Bond (Ligand Donor)	false
O3D	N	PHE- 277	2.99	145.87	H-Bond (Protein Donor)	false
O7N	O	SER- 304	2.97	147.21	H-Bond (Ligand Donor)	false
O8N	N	ASP- 306	2.87	154.35	H-Bond (Protein Donor)	false
O5B	O	HOH- 1126	3.04	144.57	H-Bond (Protein Donor)	false
O1N	O	HOH- 1135	2.66	144.09	H-Bond (Protein Donor)	false