scPDB - 2o2z entry

Protein Data Bank Entry:

PDB ID : 2o2z

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2006-11-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gluconeogenesis factor
ID:	GNGF_BACHD
AC:	Q9K706
Organism:	Bacillus halodurans
Reign:	Bacteria
TaxID:	272558
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.949
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.010	371.250

% Hydrophobic	% Polar
40.91	59.09
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	60.89 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
14.739	37.8285	162.273

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
O2N	OG1	THR- 13	2.99	152.86	H-Bond (Protein Donor)	false
C4N	CB	PRO- 185	4.15	0	Hydrophobic	false
C5D	CB	SER- 187	4.48	0	Hydrophobic	false
O3D	ND2	ASN- 217	3.3	152.35	H-Bond (Protein Donor)	false
C5N	CG2	VAL- 218	3.85	0	Hydrophobic	false
O3D	O	MET- 219	2.8	134.38	H-Bond (Ligand Donor)	false
O2D	N	MET- 219	3.36	142.84	H-Bond (Protein Donor)	false
C3D	CG	GLN- 221	3.77	0	Hydrophobic	false
N1A	NZ	LYS- 263	3.45	129	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 263	3.96	36.54	Pi/Cation	false
O1A	OH	TYR- 264	2.63	160.14	H-Bond (Protein Donor)	false
N6A	OE1	GLU- 267	3.21	147.25	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 300	3.81	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 300	3.02	167.49	H-Bond (Protein Donor)	false
O7N	N	HIS- 301	3.12	167.05	H-Bond (Protein Donor)	false
C4N	CB	HIS- 301	4.2	0	Hydrophobic	false