scPDB - 2ivu entry

Protein Data Bank Entry:

PDB ID : 2ivu

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-06-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Proto-oncogene tyrosine-protein kinase receptor Ret
ID:	RET_HUMAN
AC:	P07949
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:	33.221
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.270	489.375

% Hydrophobic	% Polar
60.69	39.31
According to VolSite

Ligand :

HET Code:	ZD6
Formula:	C22H25BrFN4O2
Molecular weight:	476.362 g/mol
DrugBank ID:	DB05294
Buried Surface Area:	59.03 %
Polar Surface area:	59.65 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-24.0954	9.9889	-11.0118

Binding mode :

What is Poseview ?

2D View
3D View

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
CAL	CD2	LEU- 730	3.78	0	Hydrophobic	false
CAO	CD1	LEU- 730	4.12	0	Hydrophobic	false
CAA	CB	LEU- 730	3.8	0	Hydrophobic	false
CAY	CD1	LEU- 730	3.58	0	Hydrophobic	false
FAC	CG1	VAL- 738	3.4	0	Hydrophobic	false
CAJ	CG1	VAL- 738	3.86	0	Hydrophobic	false
CAW	CG2	VAL- 738	3.69	0	Hydrophobic	false
C5	CB	ALA- 756	4.18	0	Hydrophobic	false
CAV	CB	ALA- 756	4.34	0	Hydrophobic	false
BR	CD	LYS- 758	3.81	0	Hydrophobic	false
CAU	CD	LYS- 758	3.6	0	Hydrophobic	false
CAH	CB	LYS- 758	3.54	0	Hydrophobic	false
BR	CG	GLU- 775	4.02	0	Hydrophobic	false
BR	CD1	LEU- 779	3.59	0	Hydrophobic	false
BR	CD1	LEU- 802	3.85	0	Hydrophobic	false
BR	CG1	VAL- 804	3.66	0	Hydrophobic	false
CAV	CG2	VAL- 804	3.44	0	Hydrophobic	false
CAK	CZ	TYR- 806	4.39	0	Hydrophobic	false
CAO	CE1	TYR- 806	3.86	0	Hydrophobic	false
CAI	CB	ALA- 807	4.42	0	Hydrophobic	false
N3	N	ALA- 807	3.08	165.55	H-Bond (Protein Donor)	false
CAF	CD1	LEU- 881	4.38	0	Hydrophobic	false
CAJ	CD2	LEU- 881	3.65	0	Hydrophobic	false