scPDB - 2i1m entry

Protein Data Bank Entry:

PDB ID : 2i1m

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-08-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

Ligand binding site composition:

B-Factor:	31.680
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.850	445.500

% Hydrophobic	% Polar
53.79	46.21
According to VolSite

Ligand :

HET Code:	5CN
Formula:	C19H21N3O3
Molecular weight:	339.388 g/mol
DrugBank ID:	DB07167
Buried Surface Area:	65.26 %
Polar Surface area:	89.5 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
46.706	42.0368	-8.0954

Binding mode :

What is Poseview ?

2D View
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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C9	CB	LEU- 588	3.95	0	Hydrophobic	false
C1	CB	LEU- 588	3.93	0	Hydrophobic	false
C5	CG	LEU- 588	3.6	0	Hydrophobic	false
C10	CG1	VAL- 596	3.95	0	Hydrophobic	false
C13	CE1	TYR- 665	4.2	0	Hydrophobic	false
O1	OH	TYR- 665	2.78	162.72	H-Bond (Ligand Donor)	false
O2	N	CYS- 666	2.86	161.48	H-Bond (Protein Donor)	false
C8	CD1	LEU- 785	3.63	0	Hydrophobic	false
C7	CG	PHE- 797	4.38	0	Hydrophobic	false
C12	CB	PHE- 797	3.98	0	Hydrophobic	false
C10	CB	ALA- 800	4.42	0	Hydrophobic	false
C12	CB	ALA- 800	4.14	0	Hydrophobic	false