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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:

3lcd

2.500 Å

X-ray

2010-01-10

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:16.784
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.945887.625

% Hydrophobic% Polar
44.4955.51
According to VolSite

Ligand :
3lcd_1 Structure
HET Code: BDY
Formula: C27H31Cl2N6O
Molecular weight: 526.481 g/mol
DrugBank ID: -
Buried Surface Area:43.74 %
Polar Surface area: 88.58 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-24.62850.224306-18.8644


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
CL12CBLEU- 5883.990Hydrophobic
C19CBLEU- 5884.40Hydrophobic
C22CD2LEU- 5883.780Hydrophobic
C23CD2LEU- 5883.480Hydrophobic
C9CG1VAL- 5963.670Hydrophobic
N1OGLU- 6643168.62H-Bond
(Ligand Donor)
N3NCYS- 6663.01178H-Bond
(Protein Donor)
CL17CD2LEU- 7853.670Hydrophobic
C16CD2LEU- 7853.770Hydrophobic
C15CD1LEU- 7853.680Hydrophobic
C15CBASP- 7964.190Hydrophobic
CL17CBASP- 7964.230Hydrophobic