scPDB - 3cp9 entry

Protein Data Bank Entry:

PDB ID : 3cp9

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-03-31

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:	31.716
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.564	779.625

% Hydrophobic	% Polar
63.20	36.80
According to VolSite

Ligand :

HET Code:	C19
Formula:	C24H23N5O
Molecular weight:	397.472 g/mol
DrugBank ID:	DB07514
Buried Surface Area:	73.55 %
Polar Surface area:	84.14 Å2

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

Mass center Coordinates

X	Y	Z
14.6371	33.7234	32.3062

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
C22	CG1	VAL- 848	3.75	0	Hydrophobic	false
C10	CG1	VAL- 848	3.55	0	Hydrophobic	false
C22	CB	ALA- 866	4.03	0	Hydrophobic	false
C3	CB	ALA- 866	3.73	0	Hydrophobic	false
C22	CB	LYS- 868	3.72	0	Hydrophobic	false
C28	CG	GLU- 885	4.01	0	Hydrophobic	false
C45	CG2	ILE- 888	4.39	0	Hydrophobic	false
C45	CD2	LEU- 889	3.99	0	Hydrophobic	false
C31	CD2	LEU- 889	3.65	0	Hydrophobic	false
C45	CD1	ILE- 892	3.88	0	Hydrophobic	false
C31	CG1	VAL- 898	4.5	0	Hydrophobic	false
C37	CG1	VAL- 898	3.46	0	Hydrophobic	false
C8	CG1	VAL- 899	3.94	0	Hydrophobic	false
C32	CB	VAL- 899	4.19	0	Hydrophobic	false
C22	CG2	THR- 916	4.09	0	Hydrophobic	false
N1	N	CYS- 919	2.98	156.46	H-Bond (Protein Donor)	false
N15	O	CYS- 919	2.75	152.24	H-Bond (Ligand Donor)	false
C37	CD1	LEU- 1019	4.32	0	Hydrophobic	false
C41	CD1	LEU- 1019	4.38	0	Hydrophobic	false
C45	SG	CYS- 1024	4.08	0	Hydrophobic	false
C11	CD1	LEU- 1035	4.33	0	Hydrophobic	false
C3	CD1	LEU- 1035	3.59	0	Hydrophobic	false
O26	N	ASP- 1046	2.98	164.58	H-Bond (Protein Donor)	false
C41	CB	ASP- 1046	4.17	0	Hydrophobic	false
C29	CB	ASP- 1046	3.58	0	Hydrophobic	false