scPDB - 3udz entry

Protein Data Bank Entry:

PDB ID : 3udz

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-10-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inositol-pentakisphosphate 2-kinase
ID:	IPPK_ARATH
AC:	Q93YN9
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	2.7.1.158

Chains:

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

Ligand binding site composition:

B-Factor:	31.965
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	3
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.588	310.500

% Hydrophobic	% Polar
67.39	32.61
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	77.37 %
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
89.9398	55.18	1.27637

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
O3B	N	ALA- 21	3.02	138.39	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 22	2.64	146.57	H-Bond (Protein Donor)	false
O3B	N	ASN- 22	2.58	144.4	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 24	3.81	0	Hydrophobic	false
O1B	CZ	ARG- 40	3.99	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 40	3.3	0	Ionic (Protein Cationic)	false
O2A	NE	ARG- 40	2.8	152.04	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 40	2.97	139.8	H-Bond (Protein Donor)	false
N6	O	ASN- 147	3.04	162.84	H-Bond (Ligand Donor)	false
N1	N	HIS- 149	3.16	154.18	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 166	2.79	152.22	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 166	3.4	149	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 166	2.62	176.19	H-Bond (Ligand Donor)	false
C2'	SD	MET- 372	4.5	0	Hydrophobic	false
C2'	CD1	ILE- 406	3.62	0	Hydrophobic	false
O1B	MG	MG- 700	2.51	0	Metal Acceptor	false
O2B	MG	MG- 701	2.77	0	Metal Acceptor	false
O1A	MG	MG- 701	2.23	0	Metal Acceptor	false