scPDB - 2vww entry

Protein Data Bank Entry:

PDB ID : 2vww

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-06-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ephrin type-B receptor 4
ID:	EPHB4_HUMAN
AC:	P54760
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:	36.466
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.125	455.625

% Hydrophobic	% Polar
57.78	42.22
According to VolSite

Ligand :

HET Code:	7X2
Formula:	C20H19ClN4O5
Molecular weight:	430.842 g/mol
DrugBank ID:	DB07250
Buried Surface Area:	59.64 %
Polar Surface area:	95.99 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
11.374	6.16933	11.6113

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
C4	CD1	ILE- 621	3.57	0	Hydrophobic	false
C14	CG1	VAL- 629	4.43	0	Hydrophobic	false
C10	CB	ALA- 645	3.34	0	Hydrophobic	false
C14	CB	ALA- 645	4.34	0	Hydrophobic	false
C16	CB	ALA- 645	3.7	0	Hydrophobic	false
C14	CG	LYS- 647	4	0	Hydrophobic	false
C16	CG	LYS- 647	4.07	0	Hydrophobic	false
C18	CD	LYS- 647	3.71	0	Hydrophobic	false
C19	CE	MET- 668	4.25	0	Hydrophobic	false
C10	CD1	ILE- 677	3.54	0	Hydrophobic	false
C21	CD1	ILE- 677	4.39	0	Hydrophobic	false
C16	CG2	THR- 693	3.94	0	Hydrophobic	false
C18	CG2	THR- 693	4.06	0	Hydrophobic	false
C1	CZ	PHE- 695	4.31	0	Hydrophobic	false
N6	O	MET- 696	2.84	132.73	H-Bond (Ligand Donor)	false
N8	N	MET- 696	2.96	158.51	H-Bond (Protein Donor)	false
C27	CB	ALA- 700	3.89	0	Hydrophobic	false
C10	CD1	LEU- 747	3.45	0	Hydrophobic	false
C24	CD2	LEU- 747	4.31	0	Hydrophobic	false
C27	CD2	LEU- 747	4.03	0	Hydrophobic	false
CL1	CD1	LEU- 747	3.75	0	Hydrophobic	false
CL1	CB	SER- 757	3.9	0	Hydrophobic	false