scPDB - 1z0z entry

Protein Data Bank Entry:

PDB ID : 1z0z

Resolution :2.850 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
B	75 %
C	25 %

Ligand binding site composition:

B-Factor:	38.670
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.652	931.500

% Hydrophobic	% Polar
42.75	57.25
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	68.08 %
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
73.1926	25.3538	105.198

Binding mode :

What is Poseview ?

2D View
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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	4.09	0	Hydrophobic	false
C5D	CD1	LEU- 53	3.39	0	Hydrophobic	false
O2A	NH1	ARG- 54	3.49	151.28	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 54	3.46	141.68	H-Bond (Protein Donor)	false
N7A	ND2	ASN- 115	3.09	164.63	H-Bond (Protein Donor)	false
O3D	ND2	ASN- 115	3.13	163.99	H-Bond (Protein Donor)	false
O3D	OE1	GLU- 116	3.05	134.59	H-Bond (Ligand Donor)	false
O3D	OE2	GLU- 116	2.93	161.54	H-Bond (Ligand Donor)	false
O2N	NZ	LYS- 126	3.3	145.13	H-Bond (Protein Donor)	false
O2N	NZ	LYS- 126	3.3	0	Ionic (Protein Cationic)	false
C3N	SD	MET- 127	3.67	0	Hydrophobic	false
C4B	CE	MET- 127	3.57	0	Hydrophobic	false
C4N	CG	MET- 127	3.64	0	Hydrophobic	false
O3B	NH1	ARG- 143	3.21	143.72	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 143	3.03	154.27	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 145	2.84	146.49	H-Bond (Ligand Donor)	false
N1A	OG1	THR- 156	2.85	165.28	H-Bond (Protein Donor)	false
C2D	CB	TYR- 158	3.79	0	Hydrophobic	false
C3N	CB	TYR- 158	4.27	0	Hydrophobic	false
O2D	N	TYR- 158	3.26	164.82	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 158	3.64	0	Aromatic Face/Face	false
N7N	O	ALA- 180	3.04	162.98	H-Bond (Ligand Donor)	false
C4B	CE2	PHE- 182	3.99	0	Hydrophobic	false
C1B	CZ	PHE- 182	3.91	0	Hydrophobic	false
O1N	NE2	GLN- 211	2.87	141.82	H-Bond (Protein Donor)	false