scPDB - 1ywn entry

Protein Data Bank Entry:

PDB ID : 1ywn

Resolution :1.710 Å

Experimental Method : X-ray

Deposition Date : 2005-02-18

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:	37.737
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.193	374.625

% Hydrophobic	% Polar
54.95	45.05
According to VolSite

Ligand :

HET Code:	LIF
Formula:	C27H19F4N5O3
Molecular weight:	537.465 g/mol
DrugBank ID:	DB04727
Buried Surface Area:	60 %
Polar Surface area:	115.3 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
0.974462	35.6062	16.0231

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
C37	CB	LEU- 838	4.37	0	Hydrophobic	false
C20	CG2	VAL- 846	4.32	0	Hydrophobic	false
C37	CB	VAL- 846	3.59	0	Hydrophobic	false
C35	CG2	VAL- 846	3.54	0	Hydrophobic	false
C30	CB	ALA- 864	3.97	0	Hydrophobic	false
C21	CD	LYS- 866	4.3	0	Hydrophobic	false
C8	CG	GLU- 883	4.33	0	Hydrophobic	false
F11	CB	GLU- 883	3.93	0	Hydrophobic	false
N12	OE2	GLU- 883	2.83	141.29	H-Bond (Ligand Donor)	false
N15	OE2	GLU- 883	2.85	131.64	H-Bond (Ligand Donor)	false
C9	CG2	ILE- 886	3.95	0	Hydrophobic	false
C6	CD2	LEU- 887	3.99	0	Hydrophobic	false
C8	CD2	LEU- 887	4.44	0	Hydrophobic	false
F3	CD1	ILE- 890	3.7	0	Hydrophobic	false
F4	CG1	VAL- 896	3.2	0	Hydrophobic	false
F4	CG1	VAL- 897	4.4	0	Hydrophobic	false
C6	CG1	VAL- 897	4.09	0	Hydrophobic	false
C17	CG2	VAL- 897	4.07	0	Hydrophobic	false
C20	CG2	VAL- 914	4.11	0	Hydrophobic	false
N31	O	GLU- 915	2.84	147.69	H-Bond (Ligand Donor)	false
N28	N	CYS- 917	2.98	171.9	H-Bond (Protein Donor)	false
F4	CD2	LEU- 1017	4.37	0	Hydrophobic	false
F3	CD1	LEU- 1017	3.52	0	Hydrophobic	false
C18	CD1	LEU- 1033	4.15	0	Hydrophobic	false
C30	CD1	LEU- 1033	3.85	0	Hydrophobic	false
F1	CG2	ILE- 1042	3.52	0	Hydrophobic	false
C17	CB	CYS- 1043	3.81	0	Hydrophobic	false
O14	N	ASP- 1044	3.07	170.3	H-Bond (Protein Donor)	false
C5	CB	ASP- 1044	3.6	0	Hydrophobic	false