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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:

3bea

2.020 Å

X-ray

2007-11-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Macrophage colony-stimulating factor 1 receptor
ID:CSF1R_HUMAN
AC:P07333
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.10.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:22.735
Number of residues:35
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.543334.125

% Hydrophobic% Polar
54.5545.45
According to VolSite

Ligand :
3bea_1 Structure
HET Code: IXH
Formula: C29H32N7O2
Molecular weight: 510.610 g/mol
DrugBank ID: -
Buried Surface Area:54.8 %
Polar Surface area: 121.06 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 6
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 5

Mass center Coordinates

XYZ
5.0406128.79566.1385


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
C9CBLEU- 5884.350Hydrophobic
C10CD1LEU- 5884.280Hydrophobic
C11CD2LEU- 5884.240Hydrophobic
C20CBLEU- 5883.720Hydrophobic
C20CBVAL- 5964.170Hydrophobic
C15CBALA- 6143.720Hydrophobic
O2NZLYS- 6162.68122.96H-Bond
(Protein Donor)
N7OG1THR- 6633.46140.57H-Bond
(Ligand Donor)
O1OG1THR- 6632.54151.17H-Bond
(Protein Donor)
N2NCYS- 6662.84165.97H-Bond
(Protein Donor)
N5OCYS- 6662.88138.84H-Bond
(Ligand Donor)
C15CD2LEU- 7853.650Hydrophobic
C27CD2LEU- 7854.350Hydrophobic
C27CBPHE- 7974.160Hydrophobic
C20CBALA- 8003.530Hydrophobic