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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:

5ar4

2.700 Å

X-ray

2015-09-24

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:5.6806.9707.6200.9107.6203

List of CHEMBLId :

CHEMBL10


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Receptor-interacting serine/threonine-protein kinase 2
ID:RIPK2_HUMAN
AC:O43353
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:42.344
Number of residues:32
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.058560.250

% Hydrophobic% Polar
45.7854.22
According to VolSite

Ligand :
5ar4_2 Structure
HET Code: SB2
Formula: C21H16FN3OS
Molecular weight: 377.435 g/mol
DrugBank ID: DB08521
Buried Surface Area:63.74 %
Polar Surface area: 77.84 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
47.527454.297623.1062


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
CB5CD1LEU- 244.340Hydrophobic
CD1CG1VAL- 324.150Hydrophobic
CD6CG2VAL- 324.360Hydrophobic
CB5CG1VAL- 323.760Hydrophobic
CB3CBALA- 453.90Hydrophobic
CD4CDLYS- 473.940Hydrophobic
CD2CBLYS- 473.560Hydrophobic
FD3CD1LEU- 703.590Hydrophobic
CB3CD2LEU- 793.890Hydrophobic
CD5CD2LEU- 793.740Hydrophobic
FD3CG2ILE- 933.270Hydrophobic
FD3CG2THR- 953.340Hydrophobic
NB1NMET- 982.91160.78H-Bond
(Protein Donor)
CB3CGMET- 984.130Hydrophobic
CA6CD2LEU- 1534.460Hydrophobic
CB3CD1LEU- 1533.560Hydrophobic
CD5CBALA- 1634.170Hydrophobic
NC3OHOH- 20112.74179.96H-Bond
(Protein Donor)