scPDB - 4uxx entry

Protein Data Bank Entry:

PDB ID : 4uxx

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2014-08-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diacylglycerol kinase
ID:	KDGL_ECOLI
AC:	P0ABN1
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.7.1.107

Chains:

Chain Name:	Percentage of Residues within binding site
B	20 %
C	80 %

Ligand binding site composition:

B-Factor:	99.999
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.013	465.750

% Hydrophobic	% Polar
55.07	44.93
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	50.56 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
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
37.1954	-31.8432	6.10616

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
C3'	CD1	TYR- 16	4.24	0	Hydrophobic	false
C4'	CZ	TYR- 16	3.34	0	Hydrophobic	false
N6	O	GLU- 85	3.26	147.98	H-Bond (Ligand Donor)	false
O2A	NZ	LYS- 94	3.12	145.86	H-Bond (Protein Donor)	false
N7	NZ	LYS- 94	3.08	138.24	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 94	3.12	0	Ionic (Protein Cationic)	false
C3'	CB	LYS- 94	3.91	0	Hydrophobic	false
O3'	OD1	ASP- 95	2.68	139.63	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 95	2.76	172.9	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 95	3.44	127.8	H-Bond (Ligand Donor)	false
O3G	ZN	ZN- 1121	2.11	0	Metal Acceptor	false
O1B	ZN	ZN- 1121	2.14	0	Metal Acceptor	false
O1G	ZN	ZN- 1122	2.22	0	Metal Acceptor	false
O1A	ZN	ZN- 1122	2.09	0	Metal Acceptor	false