scPDB - 2oh4 entry

Protein Data Bank Entry:

PDB ID : 2oh4

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2007-01-09

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:	54.505
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.182	391.500

% Hydrophobic	% Polar
71.55	28.45
According to VolSite

Ligand :

HET Code:	GIG
Formula:	C23H17F4N5O4
Molecular weight:	503.406 g/mol
DrugBank ID:	-
Buried Surface Area:	62.62 %
Polar Surface area:	117.37 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
2.46011	34.8126	16.278

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
C25	CD1	LEU- 838	4	0	Hydrophobic	false
C23	CG1	VAL- 846	3.96	0	Hydrophobic	false
C18	CG2	VAL- 846	3.8	0	Hydrophobic	false
C31	CB	ALA- 864	3.42	0	Hydrophobic	false
C23	CB	ALA- 864	3.75	0	Hydrophobic	false
C17	CD	LYS- 866	3.95	0	Hydrophobic	false
C18	CB	LYS- 866	4.3	0	Hydrophobic	false
N12	OE2	GLU- 883	2.82	134.29	H-Bond (Ligand Donor)	false
N15	OE2	GLU- 883	2.81	122.25	H-Bond (Ligand Donor)	false
F11	CG	GLU- 883	3.27	0	Hydrophobic	false
C9	CG2	ILE- 886	3.93	0	Hydrophobic	false
C6	CD2	LEU- 887	4.01	0	Hydrophobic	false
C8	CD2	LEU- 887	4.18	0	Hydrophobic	false
F1	CD1	ILE- 890	4.26	0	Hydrophobic	false
C10	CD1	ILE- 890	3.98	0	Hydrophobic	false
F1	CG1	VAL- 896	3.59	0	Hydrophobic	false
C21	CG2	VAL- 897	4.34	0	Hydrophobic	false
C6	CG1	VAL- 897	3.71	0	Hydrophobic	false
F1	CG1	VAL- 897	3.68	0	Hydrophobic	false
C31	CG2	VAL- 914	3.6	0	Hydrophobic	false
C18	CG2	VAL- 914	4.09	0	Hydrophobic	false
N32	O	CYS- 917	2.6	139.07	H-Bond (Ligand Donor)	false
N28	N	CYS- 917	2.96	169.85	H-Bond (Protein Donor)	false
F1	CD2	LEU- 1017	3.86	0	Hydrophobic	false
F3	CD1	LEU- 1017	3.37	0	Hydrophobic	false
C25	CD1	LEU- 1033	4.2	0	Hydrophobic	false
C30	CD1	LEU- 1033	3.54	0	Hydrophobic	false
F4	CG2	ILE- 1042	3.53	0	Hydrophobic	false
F1	CG2	ILE- 1042	4.46	0	Hydrophobic	false
C20	SG	CYS- 1043	4.34	0	Hydrophobic	false
C21	CB	CYS- 1043	3.83	0	Hydrophobic	false
O14	N	ASP- 1044	2.89	169.52	H-Bond (Protein Donor)	false
C8	CB	ASP- 1044	4.24	0	Hydrophobic	false
C5	CB	ASP- 1044	3.67	0	Hydrophobic	false