scPDB - 2vwy entry

Protein Data Bank Entry:

PDB ID : 2vwy

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2008-06-30

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:	21.632
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.480	462.375

% Hydrophobic	% Polar
56.93	43.07
According to VolSite

Ligand :

HET Code:	7X5
Formula:	C18H15ClN4O4S
Molecular weight:	418.854 g/mol
DrugBank ID:	DB07253
Buried Surface Area:	60.71 %
Polar Surface area:	110.82 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
11.6	6.41125	12.0344

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
C5	CD1	ILE- 621	3.6	0	Hydrophobic	false
C9	CB	ALA- 645	3.39	0	Hydrophobic	false
C12	CB	ALA- 645	4.39	0	Hydrophobic	false
C13	CB	ALA- 645	3.77	0	Hydrophobic	false
C12	CG	LYS- 647	3.93	0	Hydrophobic	false
C13	CG	LYS- 647	4.03	0	Hydrophobic	false
C14	CD	LYS- 647	3.57	0	Hydrophobic	false
C15	CE	MET- 668	4.15	0	Hydrophobic	false
C9	CD1	ILE- 677	3.59	0	Hydrophobic	false
C17	CD1	ILE- 677	4.25	0	Hydrophobic	false
C13	CG2	THR- 693	3.7	0	Hydrophobic	false
C14	CG2	THR- 693	3.8	0	Hydrophobic	false
N1	O	MET- 696	2.93	144.08	H-Bond (Ligand Donor)	false
N2	N	MET- 696	3.01	153.93	H-Bond (Protein Donor)	false
C1	CB	ALA- 700	4.13	0	Hydrophobic	false
C9	CD1	LEU- 747	3.59	0	Hydrophobic	false
CL1	CD1	LEU- 747	3.78	0	Hydrophobic	false
CL1	CB	SER- 757	3.81	0	Hydrophobic	false