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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:

4io8

2.580 Å

X-ray

2013-01-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Heat shock 70 kDa protein 1B
ID:HS71B_HUMAN
AC:P0DMV9
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:30.398
Number of residues:33
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.057475.875

% Hydrophobic% Polar
36.8863.12
According to VolSite

Ligand :
4io8_1 Structure
HET Code: 3FD
Formula: C25H23Cl2N7O4
Molecular weight: 556.401 g/mol
DrugBank ID: -
Buried Surface Area:53.64 %
Polar Surface area: 164.36 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
1.181744.8088213.9069


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
C28CE2TYR- 153.850Hydrophobic
C30CD2TYR- 153.720Hydrophobic
C33CBTHR- 373.880Hydrophobic
C32CG2THR- 373.770Hydrophobic
O26OE1GLU- 2683.08166.37H-Bond
(Ligand Donor)
O26NZLYS- 2712.72148.87H-Bond
(Protein Donor)
N10OARG- 2723.46121.77H-Bond
(Ligand Donor)
C15CDARG- 2723.940Hydrophobic
N1OGSER- 2752.69165.66H-Bond
(Protein Donor)
O27OHOH- 5242.84175.04H-Bond
(Ligand Donor)
N3OHOH- 5252.92179.97H-Bond
(Protein Donor)