scPDB - 2vwh entry

Protein Data Bank Entry:

PDB ID : 2vwh

Resolution :2.030 Å

Experimental Method : X-ray

Deposition Date : 2008-06-24

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:	GLCDH_HALMT
AC:	Q977U7
Organism:	Haloferax mediterranei
Reign:	Archaea
TaxID:	523841
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.925
Number of residues:	54
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.871	658.125

% Hydrophobic	% Polar
42.05	57.95
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	61.45 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-0.381708	29.1657	19.2939

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
O2N	N	GLY- 39	2.99	159.52	H-Bond (Protein Donor)	false
O2D	OG1	THR- 40	2.72	159.04	H-Bond (Ligand Donor)	false
C4N	CG2	ILE- 154	3.95	0	Hydrophobic	false
O1N	N	LEU- 184	3.03	154.69	H-Bond (Protein Donor)	false
C5D	CB	LEU- 184	4.16	0	Hydrophobic	false
C5N	CD2	LEU- 184	3.96	0	Hydrophobic	false
O2X	NE	ARG- 207	3.29	138.47	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 207	2.84	161.37	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 207	3.5	0	Ionic (Protein Cationic)	false
O1X	CZ	ARG- 208	3.79	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 208	3.91	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 208	2.94	170.94	H-Bond (Protein Donor)	false
O3X	NE	ARG- 208	3.03	171.7	H-Bond (Protein Donor)	false
N1A	OG	SER- 228	2.73	167.85	H-Bond (Protein Donor)	false
C5D	CB	ALA- 249	4.22	0	Hydrophobic	false
C1B	CG2	THR- 250	4.38	0	Hydrophobic	false
N7N	O	LEU- 272	2.92	173.88	H-Bond (Ligand Donor)	false
O3D	N	VAL- 274	3.2	157.18	H-Bond (Protein Donor)	false
N7N	O	SER- 301	3.07	147.84	H-Bond (Ligand Donor)	false
O7N	N	ASN- 303	2.8	168.52	H-Bond (Protein Donor)	false
O3X	O	HOH- 2074	2.84	179.96	H-Bond (Protein Donor)	false
O1N	O	HOH- 2141	2.78	179.95	H-Bond (Protein Donor)	false