scPDB - 3vo3 entry

Protein Data Bank Entry:

PDB ID : 3vo3

Resolution :1.520 Å

Experimental Method : X-ray

Deposition Date : 2012-01-19

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:	17.485
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.784	442.125

% Hydrophobic	% Polar
56.49	43.51
According to VolSite

Ligand :

HET Code:	0KF
Formula:	C22H22N7O3
Molecular weight:	432.455 g/mol
DrugBank ID:	-
Buried Surface Area:	67.58 %
Polar Surface area:	116.68 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
25.6131	-27.7085	-13.5278

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
C30	CD2	LEU- 840	3.9	0	Hydrophobic	false
C2	CG2	VAL- 848	3.7	0	Hydrophobic	false
C2	CB	ALA- 866	4.33	0	Hydrophobic	false
C3	CB	LYS- 868	3.46	0	Hydrophobic	false
C16	CG	GLU- 885	4.32	0	Hydrophobic	false
N7	OE2	GLU- 885	2.76	150.24	H-Bond (Ligand Donor)	false
C16	CG2	ILE- 888	3.57	0	Hydrophobic	false
C15	CD2	LEU- 889	3.93	0	Hydrophobic	false
C15	CG1	VAL- 898	3.86	0	Hydrophobic	false
C4	CG1	VAL- 914	4.3	0	Hydrophobic	false
C4	CG1	VAL- 916	3.58	0	Hydrophobic	false
C3	CG2	VAL- 916	3.36	0	Hydrophobic	false
C1	CG2	VAL- 916	4.03	0	Hydrophobic	false
C30	CZ	PHE- 918	4.22	0	Hydrophobic	false
C29	CE1	PHE- 918	3.91	0	Hydrophobic	false
N25	N	CYS- 919	2.99	167.02	H-Bond (Protein Donor)	false
N26	O	CYS- 919	2.78	153.19	H-Bond (Ligand Donor)	false
C6	CB	CYS- 1045	4.45	0	Hydrophobic	false
O9	N	ASP- 1046	2.95	153.11	H-Bond (Protein Donor)	false