scPDB - 1zth entry

Protein Data Bank Entry:

PDB ID : 1zth

Resolution :1.890 Å

Experimental Method : X-ray

Deposition Date : 2005-05-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	RIO-type serine/threonine-protein kinase Rio1
ID:	RIO1_ARCFU
AC:	O28471
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	2.7.11.1

Chains:

Chain Name:	Percentage of Residues within binding site
C	6 %
D	94 %

Ligand binding site composition:

B-Factor:	27.335
Number of residues:	39
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
1.166	1350.000

% Hydrophobic	% Polar
43.00	57.00
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	65.04 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-8.25907	0.798	-27.5811

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
C1'	CG2	ILE- 55	3.52	0	Hydrophobic	false
C4'	CB	SER- 56	3.76	0	Hydrophobic	false
C5'	CG2	VAL- 63	4.2	0	Hydrophobic	false
C1'	CG1	VAL- 63	4.36	0	Hydrophobic	false
O1A	NZ	LYS- 80	2.56	172.25	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 80	3.42	120.84	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 80	2.56	0	Ionic (Protein Cationic)	false
N6	O	GLU- 148	2.93	158.11	H-Bond (Ligand Donor)	false
N1	N	ILE- 150	2.77	176.51	H-Bond (Protein Donor)	false
C2'	CB	PRO- 156	4.32	0	Hydrophobic	false
C2'	SD	MET- 203	4.23	0	Hydrophobic	false
C3'	CD1	ILE- 211	3.63	0	Hydrophobic	false
O1B	MN	MN- 908	2.18	0	Metal Acceptor	false
O2A	MN	MN- 908	2.22	0	Metal Acceptor	false
O3B	O	HOH- 983	2.66	179.96	H-Bond (Protein Donor)	false