scPDB - 4z35 entry

Protein Data Bank Entry:

PDB ID : 4z35

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2015-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysophosphatidic acid receptor 1
ID:	LPAR1_HUMAN
AC:	Q92633
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:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.152	904.500

% Hydrophobic	% Polar
58.58	41.42
According to VolSite

Ligand :

HET Code:	ON9
Formula:	C32H36NO8
Molecular weight:	562.630 g/mol
DrugBank ID:	-
Buried Surface Area:	72.07 %
Polar Surface area:	127.12 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-3.2788	-26.4309	50.97

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
O	OH	TYR- 34	3.48	164.21	H-Bond (Protein Donor)	false
O	NZ	LYS- 39	2.76	121.78	H-Bond (Protein Donor)	false
O	NZ	LYS- 39	2.76	0	Ionic (Protein Cationic)	false
C28	CE1	TYR- 102	4.44	0	Hydrophobic	false
C27	CD2	LEU- 105	4.06	0	Hydrophobic	false
C23	CD1	LEU- 105	4.07	0	Hydrophobic	false
C27	CE	MET- 106	4.09	0	Hydrophobic	false
C27	CG2	THR- 109	4.28	0	Hydrophobic	false
C23	CG2	THR- 109	4.09	0	Hydrophobic	false
C24	CG2	THR- 113	4.3	0	Hydrophobic	false
O1	OG1	THR- 113	3.37	165.19	H-Bond (Protein Donor)	false
O4	NE2	GLN- 125	3	142.37	H-Bond (Protein Donor)	false
C30	CG2	ILE- 128	4.03	0	Hydrophobic	false
C28	CG2	ILE- 128	4.02	0	Hydrophobic	false
C2	CG2	ILE- 128	3.79	0	Hydrophobic	false
C30	CD2	LEU- 132	3.71	0	Hydrophobic	false
C10	CE	MET- 198	3.76	0	Hydrophobic	false
C9	SD	MET- 198	3.67	0	Hydrophobic	false
C18	CG	MET- 198	3.71	0	Hydrophobic	false
C31	CE2	TYR- 202	4.12	0	Hydrophobic	false
C31	CD2	LEU- 207	3.83	0	Hydrophobic	false
C30	CZ2	TRP- 210	4.14	0	Hydrophobic	false
O6	NE1	TRP- 210	3.29	143.57	H-Bond (Protein Donor)	false
C30	CZ3	TRP- 271	4.41	0	Hydrophobic	false
C28	CZ3	TRP- 271	3.66	0	Hydrophobic	false
C13	CD2	LEU- 277	3.78	0	Hydrophobic	false
C11	CG	LEU- 278	4.38	0	Hydrophobic	false
C10	CD2	LEU- 278	3.86	0	Hydrophobic	false
C17	CD1	LEU- 278	3.74	0	Hydrophobic	false
C	CD2	LEU- 278	4.22	0	Hydrophobic	false
C14	CB	PHE- 296	3.9	0	Hydrophobic	false
C28	CD2	LEU- 297	3.64	0	Hydrophobic	false
C27	CG	LEU- 297	3.67	0	Hydrophobic	false
C3	CD2	LEU- 297	3.58	0	Hydrophobic	false
C8	CD2	LEU- 297	3.39	0	Hydrophobic	false
C8	CD2	LEU- 297	3.39	0	Hydrophobic	false
C14	CD2	LEU- 297	4.28	0	Hydrophobic	false
C15	CB	ALA- 300	4.25	0	Hydrophobic	false