scPDB - 3b8q entry

Protein Data Bank Entry:

PDB ID : 3b8q

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2007-11-01

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
B	100 %

Ligand binding site composition:

B-Factor:	30.394
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.597	880.875

% Hydrophobic	% Polar
59.77	40.23
According to VolSite

Ligand :

HET Code:	900
Formula:	C28H21ClN2O4
Molecular weight:	484.930 g/mol
DrugBank ID:	-
Buried Surface Area:	60.88 %
Polar Surface area:	69.68 Å2

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

Mass center Coordinates

X	Y	Z
26.3919	2.88343	24.9552

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
C33	CB	LEU- 840	4.29	0	Hydrophobic	false
C27	CD1	LEU- 840	3.52	0	Hydrophobic	false
C2	CG2	VAL- 848	3.8	0	Hydrophobic	false
C26	CG1	VAL- 848	4.01	0	Hydrophobic	false
C2	CB	ALA- 866	4.42	0	Hydrophobic	false
C23	CB	ALA- 866	3.39	0	Hydrophobic	false
DuAr	NZ	LYS- 868	3.91	10.44	Pi/Cation	false
C10	CB	LYS- 868	3.41	0	Hydrophobic	false
N43	OE2	GLU- 885	3.49	133.59	H-Bond (Ligand Donor)	false
C49	CG	GLU- 885	3.7	0	Hydrophobic	false
C12	CD1	LEU- 889	3.68	0	Hydrophobic	false
C45	CD2	LEU- 889	3.81	0	Hydrophobic	false
CL54	CD1	ILE- 892	3.98	0	Hydrophobic	false
C23	CG2	VAL- 899	4.43	0	Hydrophobic	false
C11	CG1	VAL- 914	3.72	0	Hydrophobic	false
C11	CG2	THR- 916	3.64	0	Hydrophobic	false
N21	N	CYS- 919	3.14	148.55	H-Bond (Protein Donor)	false
CL54	CD2	LEU- 1019	4.45	0	Hydrophobic	false
C6	CD1	LEU- 1035	3.92	0	Hydrophobic	false
C23	CD1	LEU- 1035	3.5	0	Hydrophobic	false
C5	CB	CYS- 1045	3.52	0	Hydrophobic	false
O55	N	ASP- 1046	2.73	129.19	H-Bond (Protein Donor)	false
C45	CB	ASP- 1046	4.14	0	Hydrophobic	false
C49	CB	ASP- 1046	4.07	0	Hydrophobic	false
C33	CE2	PHE- 1047	4.07	0	Hydrophobic	false