Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4xcj

1.750 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:20.437
Number of residues:36
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.300533.250

% Hydrophobic% Polar
42.4157.59
According to VolSite

Ligand :
4xcj_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:55.67 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
18.829-12.15039.97874


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O1AND2ASN- 403.04135.54H-Bond
(Protein Donor)
N6OD2ASP- 822.81158.95H-Bond
(Ligand Donor)
C1'SDMET- 873.880Hydrophobic
C4'CBASN- 953.990Hydrophobic
C1'CBASN- 954.140Hydrophobic
C1'CD1LEU- 964.240Hydrophobic
O2ANPHE- 1282.89165.81H-Bond
(Protein Donor)
C5'CBPHE- 1284.370Hydrophobic
O2BMG MG- 3021.940Metal Acceptor
O1AMG MG- 3021.980Metal Acceptor
O1BOHOH- 4322.82179.94H-Bond
(Protein Donor)
N1OHOH- 4752.74148.18H-Bond
(Protein Donor)