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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:

4xcl

1.210 Å

X-ray

2014-12-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Heat shock cognate 90 kDa protein
ID:HSC90_DICDI
AC:P54651
Organism:Dictyostelium discoideum
Reign:Eukaryota
TaxID:44689
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:12.837
Number of residues:38
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 4
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.247540.000

% Hydrophobic% Polar
37.5062.50
According to VolSite

Ligand :
4xcl_1 Structure
HET Code: AGS
Formula: C10H14N5O12P3S
Molecular weight: 521.231 g/mol
DrugBank ID: DB02930
Buried Surface Area:52.7 %
Polar Surface area: 329.24 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
5.7484110.935946.9592


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- 402.95142.5H-Bond
(Protein Donor)
N6OD2ASP- 822.86157.21H-Bond
(Ligand Donor)
C1'SDMET- 873.880Hydrophobic
C4'CBASN- 9540Hydrophobic
C1'CBASN- 954.120Hydrophobic
C1'CD2LEU- 964.290Hydrophobic
O1ANPHE- 1282.83165.12H-Bond
(Protein Donor)
C5'CBPHE- 1284.460Hydrophobic
O1BMG MG- 3022.020Metal Acceptor
O2AMG MG- 3022.060Metal Acceptor
N1OHOH- 5012.74147.51H-Bond
(Protein Donor)
O2BOHOH- 5162.84179.96H-Bond
(Protein Donor)