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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:

4wh2

1.850 Å

X-ray

2014-09-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:N-acetylhexosamine 1-kinase
ID:NAHK_BIFL2
AC:E8MF12
Organism:Bifidobacterium longum subsp. longum
Reign:Bacteria
TaxID:565042
EC Number:2.7.1.162


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.302
Number of residues:34
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.591519.750

% Hydrophobic% Polar
42.8657.14
According to VolSite

Ligand :
4wh2_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:70.5 %
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

XYZ
5.32685-0.618111-12.388


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
C1'CE2TYR- 273.950Hydrophobic
O3BNILE- 323147H-Bond
(Protein Donor)
O2BND2ASN- 332.92146.29H-Bond
(Protein Donor)
O3BNASN- 332.82158.41H-Bond
(Protein Donor)
O2ANE2GLN- 482.98163.71H-Bond
(Protein Donor)
N6OLYS- 1033.09142.34H-Bond
(Ligand Donor)
N1NILE- 1052.84168.13H-Bond
(Protein Donor)
C2'CD1ILE- 2273.360Hydrophobic
O1BMG MG- 4022.140Metal Acceptor
O1AMG MG- 4022.010Metal Acceptor
O2BMG MG- 4032.010Metal Acceptor