scPDB - 4bb4 entry

Protein Data Bank Entry:

PDB ID : 4bb4

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2012-09-19

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:	33.701
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.316	452.250

% Hydrophobic	% Polar
51.49	48.51
According to VolSite

Ligand :

HET Code:	32W
Formula:	C23H21N5O2
Molecular weight:	399.445 g/mol
DrugBank ID:	-
Buried Surface Area:	52.19 %
Polar Surface area:	89.03 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
11.7952	8.39653	11.989

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
N	O	ILE- 621	2.71	156.4	H-Bond (Ligand Donor)	false
C	CG2	ILE- 621	4.34	0	Hydrophobic	false
C5	CB	ILE- 621	3.89	0	Hydrophobic	false
C6	CD1	ILE- 621	3.64	0	Hydrophobic	false
C14	CG1	VAL- 629	3.63	0	Hydrophobic	false
C10	CB	ALA- 645	3.31	0	Hydrophobic	false
C17	CD	LYS- 647	3.61	0	Hydrophobic	false
C17	CG2	THR- 693	3.72	0	Hydrophobic	false
N1	O	MET- 696	2.7	152.45	H-Bond (Ligand Donor)	false
N2	N	MET- 696	2.96	149.42	H-Bond (Protein Donor)	false
C14	CD2	LEU- 747	4.27	0	Hydrophobic	false
C11	CD1	LEU- 747	3.56	0	Hydrophobic	false
C12	CD1	LEU- 747	4.03	0	Hydrophobic	false