scPDB - 3v2y entry

Protein Data Bank Entry:

PDB ID : 3v2y

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2011-12-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sphingosine 1-phosphate receptor 1
ID:	S1PR1_HUMAN
AC:	P21453
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:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.321	1225.125

% Hydrophobic	% Polar
51.24	48.76
According to VolSite

Ligand :

HET Code:	ML5
Formula:	C16H26N2O4P
Molecular weight:	341.362 g/mol
DrugBank ID:	-
Buried Surface Area:	67.98 %
Polar Surface area:	129.74 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
5.68752	17.5377	-8.97848

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
O4	OH	TYR- 29	3.4	146.57	H-Bond (Protein Donor)	false
O2	NZ	LYS- 34	3.44	139.01	H-Bond (Protein Donor)	false
O2	NZ	LYS- 34	3.44	0	Ionic (Protein Cationic)	false
N2	OD1	ASN- 101	3.21	174.86	H-Bond (Ligand Donor)	false
O3	CZ	ARG- 120	3.66	0	Ionic (Protein Cationic)	false
N2	OE2	GLU- 121	3.07	0	Ionic (Ligand Cationic)	false
C7	CB	MET- 124	3.37	0	Hydrophobic	false
C3	CE	MET- 124	3.55	0	Hydrophobic	false
C1	CB	MET- 124	3.36	0	Hydrophobic	false
C7	CD2	PHE- 125	3.91	0	Hydrophobic	false
C8	CE2	PHE- 125	4.37	0	Hydrophobic	false
C10	CZ	PHE- 125	3.43	0	Hydrophobic	false
C12	CE1	PHE- 125	3.64	0	Hydrophobic	false
C9	CD2	LEU- 128	3.58	0	Hydrophobic	false
C11	CD2	LEU- 128	3.44	0	Hydrophobic	false
C12	CB	CYS- 206	3.6	0	Hydrophobic	false
C12	CD2	PHE- 210	4.3	0	Hydrophobic	false
C8	CZ3	TRP- 269	3.72	0	Hydrophobic	false
C8	CD2	LEU- 272	4.01	0	Hydrophobic	false
C10	CD2	LEU- 272	4.26	0	Hydrophobic	false
C11	CE1	PHE- 273	4.35	0	Hydrophobic	false
C11	CD1	LEU- 276	3.48	0	Hydrophobic	false
C15	CD1	LEU- 297	3.58	0	Hydrophobic	false
C6	CD2	LEU- 297	4.01	0	Hydrophobic	false
C4	CD2	LEU- 297	3.61	0	Hydrophobic	false
C3	CG2	VAL- 301	4.02	0	Hydrophobic	false
O2	O	HOH- 1210	2.99	163.46	H-Bond (Protein Donor)	false