scPDB - 4rup entry

Protein Data Bank Entry:

PDB ID : 4rup

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2014-11-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vitamin D3 receptor A
ID:	VDRA_DANRE
AC:	Q9PTN2
Organism:	Danio rerio
Reign:	Eukaryota
TaxID:	7955
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	47.386
Number of residues:	50
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.033	668.250

% Hydrophobic	% Polar
73.74	26.26
According to VolSite

Ligand :

HET Code:	H97
Formula:	C31H44F6O4
Molecular weight:	594.669 g/mol
DrugBank ID:	-
Buried Surface Area:	79.85 %
Polar Surface area:	80.92 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
2.42063	31.7668	37.1164

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
O1	OH	TYR- 175	3.3	137.17	H-Bond (Protein Donor)	false
C2	CE2	TYR- 175	4.44	0	Hydrophobic	false
C1	CE2	TYR- 179	4.06	0	Hydrophobic	false
C1	CZ	PHE- 182	4.24	0	Hydrophobic	false
F3	CD1	LEU- 255	3.52	0	Hydrophobic	false
F3	CB	LEU- 258	4.3	0	Hydrophobic	false
C11	CD2	LEU- 258	3.88	0	Hydrophobic	false
C2	CD1	LEU- 261	4.43	0	Hydrophobic	false
C4	CD1	LEU- 261	4.42	0	Hydrophobic	false
C10	CD1	LEU- 261	3.97	0	Hydrophobic	false
C18	CD2	LEU- 261	4.22	0	Hydrophobic	false
C11	CD2	LEU- 261	3.98	0	Hydrophobic	false
F6	CG1	VAL- 262	3.65	0	Hydrophobic	false
C18	CG2	VAL- 262	3.95	0	Hydrophobic	false
F5	CG2	VAL- 262	3.48	0	Hydrophobic	false
C22	CG2	VAL- 262	4.1	0	Hydrophobic	false
O2	OG	SER- 265	2.87	160.41	H-Bond (Ligand Donor)	false
F6	CD1	ILE- 296	4.43	0	Hydrophobic	false
C16	CD1	ILE- 296	4.33	0	Hydrophobic	false
C27	CD1	ILE- 296	3.9	0	Hydrophobic	false
C4	CG2	ILE- 299	4.03	0	Hydrophobic	false
C15	CG2	ILE- 299	4.43	0	Hydrophobic	false
C16	CG	MET- 300	4.1	0	Hydrophobic	false
C28	CE	MET- 300	3.53	0	Hydrophobic	false
C31	CE	MET- 300	3.4	0	Hydrophobic	false
O2	NH1	ARG- 302	2.91	157.97	H-Bond (Protein Donor)	false
C3	CG	ARG- 302	3.88	0	Hydrophobic	false
C4	CB	SER- 303	3.59	0	Hydrophobic	false
C1	CB	SER- 306	4.19	0	Hydrophobic	false
O1	OG	SER- 306	2.68	159.01	H-Bond (Ligand Donor)	false
C9	CD2	TRP- 314	3.72	0	Hydrophobic	false
C14	CZ2	TRP- 314	4.16	0	Hydrophobic	false
C10	SG	CYS- 316	3.41	0	Hydrophobic	false
C9	CD1	TYR- 323	4.41	0	Hydrophobic	false
C12	CG2	VAL- 328	3.4	0	Hydrophobic	false
C20	CG1	VAL- 328	4.34	0	Hydrophobic	false
F1	CB	ALA- 331	4.31	0	Hydrophobic	false
O3	NE2	HIS- 333	2.9	148.89	H-Bond (Protein Donor)	false
C32	CB	HIS- 333	3.97	0	Hydrophobic	false
C32	CB	HIS- 337	4.47	0	Hydrophobic	false
C32	CD2	LEU- 338	3.45	0	Hydrophobic	false
C31	CB	LEU- 341	4.16	0	Hydrophobic	false
C17	CD2	LEU- 341	4.18	0	Hydrophobic	false
C31	CD2	LEU- 419	4.24	0	Hydrophobic	false
O3	NE2	HIS- 423	2.92	166.16	H-Bond (Ligand Donor)	false
C28	CB	HIS- 423	4.31	0	Hydrophobic	false
C30	CB	HIS- 423	4.43	0	Hydrophobic	false
F2	CD1	TYR- 427	4.31	0	Hydrophobic	false
F4	CD1	TYR- 427	3.4	0	Hydrophobic	false
F2	CD1	LEU- 430	3.35	0	Hydrophobic	false
F2	CD2	LEU- 440	3.62	0	Hydrophobic	false
F4	CG1	VAL- 444	3.7	0	Hydrophobic	false
F6	CE1	PHE- 448	3.37	0	Hydrophobic	false