scPDB - 1z0u entry

Protein Data Bank Entry:

PDB ID : 1z0u

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-03-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD kinase
ID:	NADK_ARCFU
AC:	O30297
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.306
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.390	340.875

% Hydrophobic	% Polar
46.53	53.47
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	50.79 %
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
-7.06017	12.2303	14.5027

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
C2B	CB	ASP- 49	4.42	0	Hydrophobic	false
O1X	N	ASP- 49	3	154.84	H-Bond (Protein Donor)	false
O2X	N	GLY- 50	2.93	158.63	H-Bond (Protein Donor)	false
C5D	CD1	LEU- 53	3.97	0	Hydrophobic	false
O2A	CZ	ARG- 54	3.84	0	Ionic (Protein Cationic)	false
O1N	CZ	ARG- 54	3.75	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 54	3.25	150.28	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 54	2.94	135.02	H-Bond (Protein Donor)	false
N7A	ND2	ASN- 115	3.04	156.72	H-Bond (Protein Donor)	false
O3D	ND2	ASN- 115	3.04	174.87	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 115	2.81	136.34	H-Bond (Ligand Donor)	false
O3D	OE2	GLU- 116	2.68	150.62	H-Bond (Ligand Donor)	false
O3D	OE1	GLU- 116	3.19	130.04	H-Bond (Ligand Donor)	false
O2D	OE1	GLU- 116	2.58	149.79	H-Bond (Ligand Donor)	false
N6A	O	ILE- 153	3.04	156.65	H-Bond (Ligand Donor)	false
N1A	OG1	THR- 156	2.52	170.14	H-Bond (Protein Donor)	false
C2D	CB	TYR- 158	3.84	0	Hydrophobic	false
C3N	CB	TYR- 158	4.26	0	Hydrophobic	false
O2D	N	TYR- 158	3.16	148.23	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 158	3.75	0	Aromatic Face/Face	false
O1N	NE2	GLN- 211	3	145.38	H-Bond (Protein Donor)	false