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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4itm

2.200 Å

X-ray

2013-01-18

Interactomes:
Molecular Function:
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
A100 %


Ligand binding site composition:

B-Factor:22.636
Number of residues:26
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0781096.875

% Hydrophobic% Polar
46.7753.23
According to VolSite

Ligand :
4itm_1 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:59.69 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
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

XYZ
3.06106-1.317480.372516


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O1BNGLY- 502.94151.9H-Bond
(Protein Donor)
O2GNTHR- 522.76153.32H-Bond
(Protein Donor)
C2'CBTHR- 524.150Hydrophobic
N7OGSER- 532.63147.13H-Bond
(Protein Donor)
C2'CD2LEU- 1034.330Hydrophobic
O1BOHTYR- 1872.54158.06H-Bond
(Protein Donor)
O2ANH1ARG- 2063.02158.42H-Bond
(Protein Donor)
O1ANE2GLN- 2402.96157.08H-Bond
(Protein Donor)
C1'CGPRO- 2794.190Hydrophobic
N6OPHE- 2962.74170.41H-Bond
(Ligand Donor)
N1NPHE- 2962.99161.16H-Bond
(Protein Donor)
O1GOHOH- 5292.53156.5H-Bond
(Protein Donor)