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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:

2yef

1.550 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:12.998
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.208465.750

% Hydrophobic% Polar
39.1360.87
According to VolSite

Ligand :
2yef_1 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:53.12 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
4.44394-1.110847.35861


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
O2AND2ASN- 512.99135.91H-Bond
(Protein Donor)
N6OD2ASP- 932.98160.09H-Bond
(Ligand Donor)
C1'SDMET- 983.890Hydrophobic
C4'CBASN- 1064.020Hydrophobic
C1'CBASN- 1064.290Hydrophobic
C5'CD2LEU- 1074.090Hydrophobic
O2GNGLY- 1373.42154.86H-Bond
(Protein Donor)
O1ANPHE- 1382.88165.98H-Bond
(Protein Donor)
O1GMG MG- 12271.990Metal Acceptor
O1BMG MG- 12272.080Metal Acceptor
O2AMG MG- 12271.950Metal Acceptor
N1OHOH- 23152.8154.79H-Bond
(Ligand Donor)