scPDB - 1y6b entry

Protein Data Bank Entry:

PDB ID : 1y6b

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-12-05

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:	36.942
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.363	401.625

% Hydrophobic	% Polar
69.75	30.25
According to VolSite

Ligand :

HET Code:	AAX
Formula:	C25H24N4O4S
Molecular weight:	476.547 g/mol
DrugBank ID:	DB07333
Buried Surface Area:	64.46 %
Polar Surface area:	114.72 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
0.389176	30.7044	17.3174

Binding mode :

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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
C31	CB	LEU- 838	4.48	0	Hydrophobic	false
C34	CB	LEU- 838	4.34	0	Hydrophobic	false
C1	CD2	LEU- 838	4.13	0	Hydrophobic	false
C3	CD2	LEU- 838	3.72	0	Hydrophobic	false
C34	CB	VAL- 846	4.22	0	Hydrophobic	false
C18	CG2	VAL- 846	3.8	0	Hydrophobic	false
C19	CG1	VAL- 846	3.71	0	Hydrophobic	false
C19	CG1	VAL- 846	3.71	0	Hydrophobic	false
C22	CB	ALA- 864	4.24	0	Hydrophobic	false
C20	CB	ALA- 864	3.84	0	Hydrophobic	false
C23	CB	LYS- 866	3.29	0	Hydrophobic	false
N25	OE2	GLU- 883	2.54	157.76	H-Bond (Ligand Donor)	false
C21	CG2	VAL- 914	3.8	0	Hydrophobic	false
C22	CG2	VAL- 914	3.29	0	Hydrophobic	false
C1	CZ	PHE- 916	3.84	0	Hydrophobic	false
N9	O	CYS- 917	2.86	144.98	H-Bond (Ligand Donor)	false
N11	N	CYS- 917	3.03	154.78	H-Bond (Protein Donor)	false
O28	ND2	ASN- 921	2.94	173.1	H-Bond (Protein Donor)	false
C7	CD2	LEU- 1033	4.09	0	Hydrophobic	false
C15	CD1	LEU- 1033	4.12	0	Hydrophobic	false