scPDB - 2xir entry

Protein Data Bank Entry:

PDB ID : 2xir

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2010-06-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vascular endothelial growth factor receptor 2
ID:	VGFR2_HUMAN
AC:	P35968
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:	18.181
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.453	735.750

% Hydrophobic	% Polar
59.17	40.83
According to VolSite

Ligand :

HET Code:	00J
Formula:	C26H28N3O5
Molecular weight:	462.518 g/mol
DrugBank ID:	-
Buried Surface Area:	60.97 %
Polar Surface area:	87.26 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
18.9262	25.96	39.8721

Binding mode :

What is Poseview ?

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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
C20	CD1	LEU- 840	4.09	0	Hydrophobic	false
C9	CD1	LEU- 840	4.11	0	Hydrophobic	false
C18	CD2	LEU- 840	3.96	0	Hydrophobic	false
C16	CD2	LEU- 840	4.12	0	Hydrophobic	false
C3	CB	LEU- 840	3.59	0	Hydrophobic	false
C10	CG2	VAL- 848	3.51	0	Hydrophobic	false
C22	CG1	VAL- 848	3.99	0	Hydrophobic	false
C10	CB	ALA- 866	4.41	0	Hydrophobic	false
C7	CB	ALA- 866	3.48	0	Hydrophobic	false
C1	CB	LYS- 868	3.88	0	Hydrophobic	false
C1	CD1	LEU- 889	4	0	Hydrophobic	false
C1	CG1	VAL- 914	3.47	0	Hydrophobic	false
C1	CG1	VAL- 916	3.83	0	Hydrophobic	false
C10	CG2	VAL- 916	3.88	0	Hydrophobic	false
C7	CG2	VAL- 916	4	0	Hydrophobic	false
C16	CZ	PHE- 918	3.69	0	Hydrophobic	false
N27	N	CYS- 919	2.95	163.31	H-Bond (Protein Donor)	false
C4	CD1	LEU- 1035	3.97	0	Hydrophobic	false
C7	CD1	LEU- 1035	3.62	0	Hydrophobic	false
C20	CD2	LEU- 1035	3.82	0	Hydrophobic	false
C4	SG	CYS- 1045	3.73	0	Hydrophobic	false
C6	CB	CYS- 1045	3.46	0	Hydrophobic	false
O30	N	ASP- 1046	2.52	169.63	H-Bond (Protein Donor)	false