scPDB - 4dk7 entry

Protein Data Bank Entry:

PDB ID : 4dk7

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2012-02-03

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-beta
ID:	NR1H2_HUMAN
AC:	P55055
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:	55.390
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.315	1049.625

% Hydrophobic	% Polar
58.52	41.48
According to VolSite

Ligand :

HET Code:	0KS
Formula:	C16H13F6NO3S
Molecular weight:	413.335 g/mol
DrugBank ID:	-
Buried Surface Area:	78.4 %
Polar Surface area:	65.98 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
40.5217	66.7944	40.4784

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
F5	CZ	PHE- 268	4.49	0	Hydrophobic	false
F7	CE1	PHE- 268	4.37	0	Hydrophobic	false
F9	CE1	PHE- 268	4.26	0	Hydrophobic	false
F6	CB	PHE- 271	4.12	0	Hydrophobic	false
F5	CG2	THR- 272	3.48	0	Hydrophobic	false
C12	CB	LEU- 274	3.79	0	Hydrophobic	false
C19	CB	ALA- 275	4.34	0	Hydrophobic	false
C12	CB	ALA- 275	4.13	0	Hydrophobic	false
C11	CB	SER- 278	4.27	0	Hydrophobic	false
C7	CD1	ILE- 309	4.38	0	Hydrophobic	false
C5	CD1	ILE- 309	3.75	0	Hydrophobic	false
C5	SD	MET- 312	4.3	0	Hydrophobic	false
C11	CG	MET- 312	3.98	0	Hydrophobic	false
C7	CD2	LEU- 313	3.4	0	Hydrophobic	false
O4	OG1	THR- 316	2.76	172.45	H-Bond (Protein Donor)	false
C20	CD2	LEU- 345	4.39	0	Hydrophobic	false
F9	CG	LEU- 345	4.31	0	Hydrophobic	false
C4	CD1	LEU- 345	3.97	0	Hydrophobic	false
C7	CZ	PHE- 349	4.4	0	Hydrophobic	false
F8	CE2	PHE- 349	4.11	0	Hydrophobic	false
C7	CD1	ILE- 353	4.33	0	Hydrophobic	false
O1	NE2	HIS- 435	2.61	163.44	H-Bond (Protein Donor)	false
F8	CG	GLN- 438	3.29	0	Hydrophobic	false
F7	CG2	VAL- 439	4.25	0	Hydrophobic	false
F8	CG2	VAL- 439	4.11	0	Hydrophobic	false
F7	CG	LEU- 442	4.45	0	Hydrophobic	false
C20	CD1	LEU- 442	3.82	0	Hydrophobic	false
C19	CD2	LEU- 449	4.31	0	Hydrophobic	false
F7	CD2	LEU- 449	3.57	0	Hydrophobic	false
F4	CD1	LEU- 453	3.66	0	Hydrophobic	false
F4	CZ3	TRP- 457	3.83	0	Hydrophobic	false