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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:

2yjw

1.610 Å

X-ray

2011-05-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Heat shock protein HSP 90-alpha
ID:HS90A_HUMAN
AC:P07900
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:13.297
Number of residues:32
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.335367.875

% Hydrophobic% Polar
44.9555.05
According to VolSite

Ligand :
2yjw_1 Structure
HET Code: YJW
Formula: C16H13NO3
Molecular weight: 267.279 g/mol
DrugBank ID: -
Buried Surface Area:69.28 %
Polar Surface area: 66.49 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
0.984635.182624.8082


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
C13CBASN- 513.990Hydrophobic
C23CBASN- 513.410Hydrophobic
C13CBASP- 544.140Hydrophobic
C21CBALA- 554.210Hydrophobic
C8CDLYS- 583.870Hydrophobic
O30OD2ASP- 932.66160.56H-Bond
(Ligand Donor)
O30OD1ASP- 933.32125.49H-Bond
(Ligand Donor)
C8CG2ILE- 963.80Hydrophobic
C8CGMET- 984.420Hydrophobic
C25CEMET- 983.70Hydrophobic
C15CG2THR- 1094.040Hydrophobic
N2OG1THR- 1843.22141.73H-Bond
(Protein Donor)
C22CG2THR- 1843.870Hydrophobic
C23CG2VAL- 1864.080Hydrophobic