scPDB - 3x04 entry

Protein Data Bank Entry:

PDB ID : 3x04

Resolution :2.600 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:	68.220
Number of residues:	20
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.525	712.125

% Hydrophobic	% Polar
56.87	43.13
According to VolSite

Ligand :

HET Code:	GNP
Formula:	C10H13N6O13P3
Molecular weight:	518.164 g/mol
DrugBank ID:	DB02082
Buried Surface Area:	41.19 %
Polar Surface area:	338.36 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
44.8613	61.7976	-5.16803

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'	CZ	PHE- 139	3.94	0	Hydrophobic	false
O2B	NZ	LYS- 150	3.93	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 150	3.25	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 150	3.25	168.05	H-Bond (Protein Donor)	false
N1	OD1	ASN- 203	2.78	165.8	H-Bond (Ligand Donor)	false
O6	N	VAL- 204	3.19	155.2	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 214	2.92	160.59	H-Bond (Protein Donor)	false
O3'	OG1	THR- 237	3.49	160.99	H-Bond (Ligand Donor)	false