scPDB - 2x2k entry

Protein Data Bank Entry:

PDB ID : 2x2k

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2010-01-13

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:	38.263
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.085	391.500

% Hydrophobic	% Polar
58.62	41.38
According to VolSite

Ligand :

HET Code:	X2K
Formula:	C15H15N3O
Molecular weight:	253.299 g/mol
DrugBank ID:	-
Buried Surface Area:	62.23 %
Polar Surface area:	70.91 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
-11.286	8.42916	11.1399

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
CAB	CB	LEU- 730	4.24	0	Hydrophobic	false
CAA	CD2	LEU- 730	3.9	0	Hydrophobic	false
CAS	CG1	VAL- 738	3.82	0	Hydrophobic	false
CAI	CG2	VAL- 738	3.57	0	Hydrophobic	false
CAG	CB	ALA- 756	4.45	0	Hydrophobic	false
CAG	CG1	ILE- 788	4.21	0	Hydrophobic	false
CAG	CG2	VAL- 804	3.49	0	Hydrophobic	false
NAK	O	GLU- 805	3.07	165.88	H-Bond (Ligand Donor)	false
CAA	CE1	TYR- 806	3.78	0	Hydrophobic	false
OAD	N	ALA- 807	3.12	155.27	H-Bond (Protein Donor)	false
CAS	CD1	LEU- 881	3.53	0	Hydrophobic	false
CAI	CD2	LEU- 881	3.84	0	Hydrophobic	false
CAG	CD1	LEU- 881	3.65	0	Hydrophobic	false
CAF	CB	SER- 891	4.16	0	Hydrophobic	false