scPDB - 2xvd entry

Protein Data Bank Entry:

PDB ID : 2xvd

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2010-10-25

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:	37.524
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.107	860.625

% Hydrophobic	% Polar
45.10	54.90
According to VolSite

Ligand :

HET Code:	AS6
Formula:	C26H33N5O4S
Molecular weight:	511.636 g/mol
DrugBank ID:	-
Buried Surface Area:	58.65 %
Polar Surface area:	116.27 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:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
11.4724	6.97217	11.356

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
C9	CD1	ILE- 621	3.61	0	Hydrophobic	false
C2	CG1	VAL- 629	3.79	0	Hydrophobic	false
C3	CG2	VAL- 629	3.46	0	Hydrophobic	false
C14	CG1	VAL- 629	3.38	0	Hydrophobic	false
C5	CB	ALA- 645	3.39	0	Hydrophobic	false
C26	CB	ALA- 645	3.54	0	Hydrophobic	false
C3	CD	LYS- 647	3.89	0	Hydrophobic	false
C26	CB	LYS- 647	4.03	0	Hydrophobic	false
C24	CD	LYS- 647	3.85	0	Hydrophobic	false
O4	OE2	GLU- 664	2.79	128.53	H-Bond (Ligand Donor)	false
C23	CE	MET- 668	4.1	0	Hydrophobic	false
C24	CG2	ILE- 691	4.27	0	Hydrophobic	false
C5	CB	THR- 693	4.35	0	Hydrophobic	false
C24	CG2	THR- 693	3.45	0	Hydrophobic	false
C15	CZ	PHE- 695	4.36	0	Hydrophobic	false
N2	N	MET- 696	3.01	138.98	H-Bond (Protein Donor)	false
N3	O	MET- 696	2.95	145.15	H-Bond (Ligand Donor)	false
C1	CD2	LEU- 747	4	0	Hydrophobic	false
C5	CD1	LEU- 747	3.45	0	Hydrophobic	false
C20	CD1	LEU- 747	4.28	0	Hydrophobic	false
C22	CB	SER- 757	3.71	0	Hydrophobic	false
O4	N	ASP- 758	2.86	166.7	H-Bond (Protein Donor)	false