scPDB - 2vwu entry

Protein Data Bank Entry:

PDB ID : 2vwu

Resolution :2.000 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:	24.188
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.064	502.875

% Hydrophobic	% Polar
53.69	46.31
According to VolSite

Ligand :

HET Code:	7X1
Formula:	C24H28ClN4O4
Molecular weight:	471.957 g/mol
DrugBank ID:	DB07249
Buried Surface Area:	53.26 %
Polar Surface area:	79.17 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.1111	8.48633	11.6276

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	ILE- 621	3.81	0	Hydrophobic	false
C23	CD1	ILE- 621	3.45	0	Hydrophobic	false
C1	CG1	VAL- 629	4.41	0	Hydrophobic	false
C4	CG1	VAL- 629	4	0	Hydrophobic	false
C5	CB	ALA- 645	3.95	0	Hydrophobic	false
C9	CB	ALA- 645	4.47	0	Hydrophobic	false
C11	CB	ALA- 645	3.93	0	Hydrophobic	false
C9	CG	LYS- 647	3.92	0	Hydrophobic	false
C11	CG	LYS- 647	3.79	0	Hydrophobic	false
C13	CD	LYS- 647	3.75	0	Hydrophobic	false
DuAr	NZ	LYS- 647	3.93	157.46	Pi/Cation	false
C14	CE	MET- 668	3.79	0	Hydrophobic	false
CL1	CD1	ILE- 677	4.47	0	Hydrophobic	false
C16	CD1	ILE- 677	4.16	0	Hydrophobic	false
C13	CG2	ILE- 691	4.41	0	Hydrophobic	false
C11	CG2	THR- 693	3.98	0	Hydrophobic	false
C13	CG2	THR- 693	3.64	0	Hydrophobic	false
N18	OG1	THR- 693	3.04	136.7	H-Bond (Protein Donor)	false
C25	CZ	PHE- 695	3.91	0	Hydrophobic	false
N20	N	MET- 696	3.03	154.06	H-Bond (Protein Donor)	false
C22	CB	MET- 696	4.35	0	Hydrophobic	false
C4	CD2	LEU- 747	4.34	0	Hydrophobic	false
C5	CD1	LEU- 747	3.9	0	Hydrophobic	false
CL1	CD1	LEU- 747	3.71	0	Hydrophobic	false
C16	CD1	LEU- 747	4.47	0	Hydrophobic	false
CL1	CB	SER- 757	3.75	0	Hydrophobic	false