scPDB - 4ehy entry

Protein Data Bank Entry:

PDB ID : 4ehy

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-04-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tetraacyldisaccharide 4'-kinase
ID:	LPXK_AQUAE
AC:	O67572
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	50.205
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	CL MG

Cavity properties

Ligandability	Volume (Å3)
0.936	600.750

% Hydrophobic	% Polar
46.63	53.37
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	82.91 %
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
6.15426	-5.44189	1.22215

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
O2B	OG	SER- 49	3.31	141.5	H-Bond (Protein Donor)	false
O2B	N	SER- 49	2.9	140.79	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 51	3.79	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 51	2.96	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 51	2.96	152.18	H-Bond (Protein Donor)	false
O2B	N	LYS- 51	3.44	150.68	H-Bond (Protein Donor)	false
O3B	N	THR- 52	2.82	164.26	H-Bond (Protein Donor)	false
O3B	OG1	THR- 52	2.62	154.77	H-Bond (Protein Donor)	false
C5'	CB	THR- 52	4.07	0	Hydrophobic	false
O3'	OG	SER- 53	3.2	147.07	H-Bond (Ligand Donor)	false
N7	NH1	ARG- 206	3.36	123.95	H-Bond (Protein Donor)	false
C1'	CD2	LEU- 235	4.06	0	Hydrophobic	false
O2A	N	GLY- 236	2.89	163.87	H-Bond (Protein Donor)	false
N7	NE2	GLN- 240	2.75	166.14	H-Bond (Protein Donor)	false
N6	OE1	GLN- 240	2.92	169.44	H-Bond (Ligand Donor)	false
C1'	CB	THR- 278	3.71	0	Hydrophobic	false
O2A	NZ	LYS- 280	2.97	146.7	H-Bond (Protein Donor)	false
O2'	N	LYS- 280	3.39	124.36	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 280	2.97	0	Ionic (Protein Cationic)	false
C4'	CD	LYS- 280	3.92	0	Hydrophobic	false
C1'	CB	LYS- 280	3.86	0	Hydrophobic	false
C3'	CZ	PHE- 296	4.4	0	Hydrophobic	false
C2'	CE2	PHE- 296	4.11	0	Hydrophobic	false
O1B	MG	MG- 403	2.09	0	Metal Acceptor	false
O1A	O	HOH- 506	2.76	179.96	H-Bond (Protein Donor)	false