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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:

1uym

2.450 Å

X-ray

2004-03-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Heat shock protein HSP 90-beta
ID:HS90B_HUMAN
AC:P08238
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:52.089
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.224810.000

% Hydrophobic% Polar
48.7551.25
According to VolSite

Ligand :
1uym_1 Structure
HET Code: PU3
Formula: C19H25N5O3
Molecular weight: 371.433 g/mol
DrugBank ID: DB02754
Buried Surface Area:60.61 %
Polar Surface area: 97.31 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
3.6075211.134424.759


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
C9CBASN- 514.290Hydrophobic
N5OD2ASP- 932.66160.87H-Bond
(Ligand Donor)
C8SDMET- 984.450Hydrophobic
C15SDMET- 983.960Hydrophobic
C2SDMET- 983.970Hydrophobic
C8CD2LEU- 1033.890Hydrophobic
C15CD1LEU- 1073.590Hydrophobic
C17CD2LEU- 1073.850Hydrophobic
C3CD1LEU- 1073.680Hydrophobic
C19CBALA- 1113.680Hydrophobic
C7CE2PHE- 1383.850Hydrophobic
C8CZPHE- 1383.560Hydrophobic
C6CBPHE- 1383.490Hydrophobic
C1CBPHE- 1383.590Hydrophobic
C19CE2TYR- 1393.950Hydrophobic
C7CZTYR- 1393.850Hydrophobic
C8CG2VAL- 1503.50Hydrophobic
C7CZ2TRP- 1623.860Hydrophobic
C8CD2TRP- 1623.90Hydrophobic