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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:

2yec

2.100 Å

X-ray

2011-03-25

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:27.426
Number of residues:26
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.361455.625

% Hydrophobic% Polar
42.2257.78
According to VolSite

Ligand :
2yec_1 Structure
HET Code: XQ0
Formula: C8H8N2O
Molecular weight: 148.162 g/mol
DrugBank ID: -
Buried Surface Area:68.4 %
Polar Surface area: 48.91 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
31.646711.314923.7619


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
N1ND2ASN- 512.86149.47H-Bond
(Protein Donor)
C5CBASN- 513.580Hydrophobic
C3CBALA- 553.840Hydrophobic
O3OD2ASP- 932.62174.48H-Bond
(Ligand Donor)
C1CEMET- 983.750Hydrophobic
C8CBLEU- 1073.660Hydrophobic
C8CG2THR- 1094.330Hydrophobic
C8CBPHE- 1383.590Hydrophobic
C3CG2THR- 1843.70Hydrophobic
O3OHOH- 21612.52124.24H-Bond
(Protein Donor)