scPDB - 3ipq entry

Protein Data Bank Entry:

PDB ID : 3ipq

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-08-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxysterols receptor LXR-alpha
ID:	NR1H3_HUMAN
AC:	Q13133
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:	28.637
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.690	590.625

% Hydrophobic	% Polar
73.71	26.29
According to VolSite

Ligand :

HET Code:	965
Formula:	C33H31ClF3NO3
Molecular weight:	582.052 g/mol
DrugBank ID:	DB03791
Buried Surface Area:	81.52 %
Polar Surface area:	53.8 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
41.3104	16.4236	-5.17471

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
CL4	CE1	PHE- 254	4.2	0	Hydrophobic	false
F41	CZ	PHE- 254	4.22	0	Hydrophobic	false
C25	CD1	PHE- 257	4.42	0	Hydrophobic	false
CL4	CB	PHE- 257	4.35	0	Hydrophobic	false
CL4	CG2	THR- 258	3.87	0	Hydrophobic	false
F41	CG2	THR- 258	4.19	0	Hydrophobic	false
C33	CB	LEU- 260	4.18	0	Hydrophobic	false
C25	CB	LEU- 260	3.84	0	Hydrophobic	false
C26	CB	ALA- 261	4.38	0	Hydrophobic	false
C23	CB	ALA- 261	3.99	0	Hydrophobic	false
C34	CG1	VAL- 263	4.49	0	Hydrophobic	false
C31	CB	SER- 264	3.7	0	Hydrophobic	false
C22	CD1	ILE- 295	3.9	0	Hydrophobic	false
C04	CD1	ILE- 295	3.75	0	Hydrophobic	false
C29	CE	MET- 298	4.46	0	Hydrophobic	false
C26	CE	MET- 298	4.3	0	Hydrophobic	false
C02	CE	MET- 298	4.43	0	Hydrophobic	false
C23	CE	MET- 298	3.56	0	Hydrophobic	false
C03	CB	MET- 298	3.85	0	Hydrophobic	false
C04	CD2	LEU- 299	3.62	0	Hydrophobic	false
C30	CB	GLU- 301	4.05	0	Hydrophobic	false
C15	CG2	THR- 302	4.23	0	Hydrophobic	false
C03	CB	THR- 302	4.14	0	Hydrophobic	false
O37	NE	ARG- 305	2.86	144.23	H-Bond (Protein Donor)	false
O36	NH2	ARG- 305	3.03	156.35	H-Bond (Protein Donor)	false
O37	CZ	ARG- 305	3.74	0	Ionic (Protein Cationic)	false
O36	CZ	ARG- 305	3.73	0	Ionic (Protein Cationic)	false
C31	CD	ARG- 305	4.26	0	Hydrophobic	false
C14	CD1	ILE- 313	3.75	0	Hydrophobic	false
C26	CE1	PHE- 315	3.88	0	Hydrophobic	false
C25	CZ	PHE- 315	4.04	0	Hydrophobic	false
C33	CB	PHE- 315	4.38	0	Hydrophobic	false
C28	CD1	PHE- 315	3.42	0	Hydrophobic	false
O37	N	LEU- 316	2.87	171.06	H-Bond (Protein Donor)	false
C34	CD2	LEU- 316	3.91	0	Hydrophobic	false
C07	CE1	PHE- 326	3.97	0	Hydrophobic	false
C12	CB	PHE- 326	4.3	0	Hydrophobic	false
DuAr	DuAr	PHE- 326	3.87	0	Aromatic Face/Face	false
CL4	CD2	LEU- 331	4.18	0	Hydrophobic	false
F42	CD2	LEU- 331	3.87	0	Hydrophobic	false
C11	CD1	LEU- 331	4.06	0	Hydrophobic	false
F42	CE2	PHE- 335	4.02	0	Hydrophobic	false
C13	CG2	ILE- 336	4	0	Hydrophobic	false
C12	CG1	ILE- 336	3.87	0	Hydrophobic	false
C13	CB	ILE- 339	3.83	0	Hydrophobic	false
C06	CD1	ILE- 339	3.64	0	Hydrophobic	false
C14	CG2	ILE- 339	3.41	0	Hydrophobic	false
C12	CD1	ILE- 339	3.76	0	Hydrophobic	false
F42	CG	GLN- 424	3.68	0	Hydrophobic	false
F40	CG2	VAL- 425	3.82	0	Hydrophobic	false
F41	CD1	LEU- 428	3.65	0	Hydrophobic	false
F41	CD2	LEU- 435	3.28	0	Hydrophobic	false
F40	CZ3	TRP- 443	4.06	0	Hydrophobic	false
C21	CZ3	TRP- 443	3.47	0	Hydrophobic	false