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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:

1w1s

2.000 Å

X-ray

2004-06-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cytokinin dehydrogenase 1
ID:CKX1_MAIZE
AC:Q9T0N8
Organism:Zea mays
Reign:Eukaryota
TaxID:4577
EC Number:1.5.99.12


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:15.347
Number of residues:28
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.282462.375

% Hydrophobic% Polar
64.2335.77
According to VolSite

Ligand :
1w1s_1 Structure
HET Code: EMU
Formula: C12H11N5
Molecular weight: 225.249 g/mol
DrugBank ID: -
Buried Surface Area:62.83 %
Polar Surface area: 66.48 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
71.397633.969421.5048


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
N10OD2ASP- 1693.21138.26H-Bond
(Ligand Donor)
C13CD1ILE- 1843.740Hydrophobic
C9CZ3TRP- 3973.990Hydrophobic
C11CD1ILE- 4294.340Hydrophobic
C13CBSER- 4563.740Hydrophobic
C9CD1LEU- 4583.670Hydrophobic
C14CD1LEU- 4923.550Hydrophobic
C9C6FAD- 15353.390Hydrophobic
N10O4FAD- 15353.15125.04H-Bond
(Ligand Donor)
N7OHOH- 22822.83179.95H-Bond
(Protein Donor)