scPDB - 3x0c entry

Protein Data Bank Entry:

PDB ID : 3x0c

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2014-10-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
ID:	PI42B_HUMAN
AC:	P78356
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.1.149

Chains:

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

Ligand binding site composition:

B-Factor:	73.545
Number of residues:	21
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.247	725.625

% Hydrophobic	% Polar
46.51	53.49
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	44.08 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
43.4383	60.9597	-2.77371

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'	CE2	PHE- 139	4.28	0	Hydrophobic	false
O3P	NZ	LYS- 150	2.52	127.34	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 150	2.52	0	Ionic (Protein Cationic)	false
N2	OD1	ASN- 203	3.5	124.59	H-Bond (Ligand Donor)	false
O6	N	VAL- 204	3.32	166.03	H-Bond (Protein Donor)	false
C2'	CD	LYS- 214	4.46	0	Hydrophobic	false
O2'	NZ	LYS- 214	2.63	170.24	H-Bond (Protein Donor)	false
O3'	OG1	THR- 237	2.78	139.94	H-Bond (Ligand Donor)	false
C2'	CD1	LEU- 282	4.17	0	Hydrophobic	false