scPDB - 3t9d entry

Protein Data Bank Entry:

PDB ID : 3t9d

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2011-08-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
ID:	VIP2_HUMAN
AC:	O43314
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.668
Number of residues:	39
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	3
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.223	1123.875

% Hydrophobic	% Polar
32.73	67.27
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	73.82 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
6.03526	8.49103	9.39839

Binding mode :

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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	NH2	ARG- 134	3.37	173.33	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 134	3.11	151.88	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 134	3.9	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 187	2.85	125.03	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 187	2.85	0	Ionic (Protein Cationic)	false
O1B	ND1	HIS- 194	2.81	164.15	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 211	3.59	0	Hydrophobic	false
O2G	NH2	ARG- 213	3.05	136.93	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 213	2.76	153.54	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 213	3.33	0	Ionic (Protein Cationic)	false
N6	OE1	GLU- 237	2.8	165.05	H-Bond (Ligand Donor)	false
N6	O	GLU- 238	2.97	144.55	H-Bond (Ligand Donor)	false
N1	N	MET- 240	2.83	178.95	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 246	3	125.68	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 246	2.54	166.65	H-Bond (Ligand Donor)	false
O1G	NZ	LYS- 248	3.15	0	Ionic (Protein Cationic)	false
O2'	OG	SER- 264	2.98	155.03	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 311	4.28	0	Hydrophobic	false
C3'	SG	CYS- 320	4.31	0	Hydrophobic	false
O1G	ND2	ASN- 323	3.48	151.04	H-Bond (Protein Donor)	false
O2B	MG	MG- 601	2.1	0	Metal Acceptor	false
O1G	MG	MG- 602	1.91	0	Metal Acceptor	false
O2A	MG	MG- 602	1.95	0	Metal Acceptor	false