scPDB - 3vt9 entry

Protein Data Bank Entry:

PDB ID : 3vt9

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2012-05-19

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
ID:	VDR_RAT
AC:	P13053
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.630
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.830	992.250

% Hydrophobic	% Polar
66.33	33.67
According to VolSite

Ligand :

HET Code:	YI4
Formula:	C31H50O4
Molecular weight:	486.726 g/mol
DrugBank ID:	-
Buried Surface Area:	66.87 %
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:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
13.5191	5.41837	23.9488

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
C01	CE2	TYR- 143	4.19	0	Hydrophobic	false
C03	CE2	TYR- 143	4.04	0	Hydrophobic	false
C33	CE2	TYR- 143	3.77	0	Hydrophobic	false
O02	OH	TYR- 143	2.75	156.72	H-Bond (Protein Donor)	false
C33	CE1	TYR- 147	4.31	0	Hydrophobic	false
C03	CZ	TYR- 147	3.88	0	Hydrophobic	false
C33	CE1	PHE- 150	3.73	0	Hydrophobic	false
C04	CZ	PHE- 150	4.17	0	Hydrophobic	false
C26	CD1	LEU- 223	3.59	0	Hydrophobic	false
C18	CD2	LEU- 226	4.49	0	Hydrophobic	false
C12	CD1	LEU- 226	4.45	0	Hydrophobic	false
C18	CD2	LEU- 229	4.44	0	Hydrophobic	false
C10	CD1	LEU- 229	4.17	0	Hydrophobic	false
C18	CG2	VAL- 230	4.12	0	Hydrophobic	false
C24	CG2	VAL- 230	3.68	0	Hydrophobic	false
O01	OG	SER- 233	2.74	151.92	H-Bond (Ligand Donor)	false
C22	CD1	ILE- 264	4.43	0	Hydrophobic	false
C16	CD1	ILE- 264	4.34	0	Hydrophobic	false
C15	CG2	ILE- 267	3.85	0	Hydrophobic	false
C10	CG2	ILE- 267	4.22	0	Hydrophobic	false
C21	CE	MET- 268	4.25	0	Hydrophobic	false
C16	CG	MET- 268	4.2	0	Hydrophobic	false
C01	CG	ARG- 270	3.97	0	Hydrophobic	false
O01	NH1	ARG- 270	2.69	140.35	H-Bond (Protein Donor)	false
C10	CB	SER- 271	4.34	0	Hydrophobic	false
C03	CB	SER- 274	4.23	0	Hydrophobic	false
O02	OG	SER- 274	2.96	165.72	H-Bond (Ligand Donor)	false
C11	CB	TYR- 291	3.88	0	Hydrophobic	false
C09	CD1	TYR- 291	4.03	0	Hydrophobic	false
C21	CG1	VAL- 296	4.38	0	Hydrophobic	false
C12	CG2	VAL- 296	3.58	0	Hydrophobic	false
C26	CB	ALA- 299	4.21	0	Hydrophobic	false
O03	NE2	HIS- 301	2.7	173.25	H-Bond (Protein Donor)	false
C21	CD2	LEU- 305	3.62	0	Hydrophobic	false
C21	CD2	LEU- 309	4.38	0	Hydrophobic	false
C17	CD2	LEU- 309	4.35	0	Hydrophobic	false
O03	NE2	HIS- 393	2.87	152.9	H-Bond (Ligand Donor)	false
C27	CD1	TYR- 397	4.11	0	Hydrophobic	false
C26	CD2	LEU- 400	4.34	0	Hydrophobic	false
C27	CD2	LEU- 410	4.24	0	Hydrophobic	false
C27	CG1	VAL- 414	4.46	0	Hydrophobic	false
C27	CE1	PHE- 418	4.32	0	Hydrophobic	false
O04	O	HOH- 602	2.81	162.34	H-Bond (Ligand Donor)	false