scPDB - 2if8 entry

Protein Data Bank Entry:

PDB ID : 2if8

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2006-09-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inositol polyphosphate multikinase
ID:	IPMK_YEAST
AC:	P07250
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.7.1.151

Chains:

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

Ligand binding site composition:

B-Factor:	38.915
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.907	276.750

% Hydrophobic	% Polar
65.85	34.15
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	47.09 %
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
24.0201	71.0879	43.4234

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
O1B	NZ	LYS- 31	2.93	175.33	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 31	2.93	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 31	3.89	0	Ionic (Protein Cationic)	false
N6	O	GLU- 118	2.8	143.17	H-Bond (Ligand Donor)	false
N1	N	LEU- 120	2.85	155.03	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 131	2.83	168.74	H-Bond (Ligand Donor)	false
C2'	CD1	LEU- 260	3.95	0	Hydrophobic	false
C3'	CD1	ILE- 324	3.87	0	Hydrophobic	false
O2A	MN	MN- 402	2.07	0	Metal Acceptor	false