scPDB - 3oe9 entry

Protein Data Bank Entry:

PDB ID : 3oe9

Resolution :3.100 Å

Experimental Method : X-ray

Deposition Date : 2010-08-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	C-X-C chemokine receptor type 4
ID:	CXCR4_HUMAN
AC:	P61073
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.183	675.000

% Hydrophobic	% Polar
39.00	61.00
According to VolSite

Ligand :

HET Code:	ITD
Formula:	C21H36N4S2
Molecular weight:	408.667 g/mol
DrugBank ID:	-
Buried Surface Area:	51.12 %
Polar Surface area:	93.81 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	3
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
19.6195	5.26374	28.9219

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
C14	CD	LYS- 38	3.9	0	Hydrophobic	false
S1	CZ3	TRP- 94	3.55	0	Hydrophobic	false
C3	CH2	TRP- 94	4.08	0	Hydrophobic	false
C17	CZ3	TRP- 94	4.08	0	Hydrophobic	false
C18	CZ2	TRP- 94	3.42	0	Hydrophobic	false
C19	CE2	TRP- 94	4.19	0	Hydrophobic	false
N4	OD1	ASP- 97	2.78	140.75	H-Bond (Ligand Donor)	false
C20	CZ3	TRP- 102	3.99	0	Hydrophobic	false
C19	CG1	VAL- 112	3.56	0	Hydrophobic	false
C1	CE2	TYR- 116	3.99	0	Hydrophobic	false
C3	CE2	TYR- 116	3.73	0	Hydrophobic	false
C11	CG2	ILE- 185	4.22	0	Hydrophobic	false
C12	CD1	ILE- 185	4.18	0	Hydrophobic	false
C21	SG	CYS- 186	4.34	0	Hydrophobic	false
S2	CB	ASP- 187	3.37	0	Hydrophobic	false
N1	OE1	GLU- 288	2.79	149.9	H-Bond (Protein Donor)	false