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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:

4xc0

1.770 Å

X-ray

2014-12-17

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:18.796
Number of residues:36
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.312560.250

% Hydrophobic% Polar
37.3562.65
According to VolSite

Ligand :
4xc0_1 Structure
HET Code: ACP
Formula: C11H14N5O12P3
Molecular weight: 501.176 g/mol
DrugBank ID: DB03909
Buried Surface Area:55.16 %
Polar Surface area: 310.64 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
17.203910.521775.7312


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- 402.91135.71H-Bond
(Protein Donor)
N6OD2ASP- 822.86157H-Bond
(Ligand Donor)
C1'SDMET- 873.80Hydrophobic
C4'CBASN- 953.860Hydrophobic
C1'CBASN- 954.140Hydrophobic
O3GNGLY- 1272.99160.02H-Bond
(Protein Donor)
O1ANPHE- 1282.87160.13H-Bond
(Protein Donor)
C5'CBPHE- 1284.50Hydrophobic
O1GMG MG- 3021.970Metal Acceptor
O1BMG MG- 3022.020Metal Acceptor
O2AMG MG- 3021.950Metal Acceptor
N1OHOH- 4402.69149.94H-Bond
(Protein Donor)