scPDB - 3vtd entry

Protein Data Bank Entry:

PDB ID : 3vtd

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2012-05-26

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:	42.591
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.815	799.875

% Hydrophobic	% Polar
63.29	36.71
According to VolSite

Ligand :

HET Code:	TKD
Formula:	C36H52O3
Molecular weight:	532.796 g/mol
DrugBank ID:	-
Buried Surface Area:	72.6 %
Polar Surface area:	60.69 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	7
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
12.4079	1.47279	25.7203

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
C03	CE2	TYR- 143	4.11	0	Hydrophobic	false
C01	CE2	TYR- 143	4.45	0	Hydrophobic	false
O02	OH	TYR- 143	2.97	155.21	H-Bond (Protein Donor)	false
C03	CE2	TYR- 147	4.23	0	Hydrophobic	false
C04	CZ	PHE- 150	4.01	0	Hydrophobic	false
C35	CD1	LEU- 223	4.38	0	Hydrophobic	false
C36	CD1	LEU- 223	3.31	0	Hydrophobic	false
C11	CD2	LEU- 226	4.07	0	Hydrophobic	false
C33	CB	LEU- 226	4.31	0	Hydrophobic	false
C38	CB	ALA- 227	4.31	0	Hydrophobic	false
C04	CD1	LEU- 229	4.32	0	Hydrophobic	false
C18	CG2	VAL- 230	3.73	0	Hydrophobic	false
C38	CG2	VAL- 230	3.66	0	Hydrophobic	false
O01	OG	SER- 233	2.71	159.62	H-Bond (Ligand Donor)	false
C22	CD1	ILE- 264	4.31	0	Hydrophobic	false
C23	CD1	ILE- 264	3.98	0	Hydrophobic	false
C15	CG2	ILE- 267	4.17	0	Hydrophobic	false
C10	CG2	ILE- 267	4.17	0	Hydrophobic	false
C22	CE	MET- 268	3.66	0	Hydrophobic	false
C16	CG	MET- 268	3.88	0	Hydrophobic	false
C01	CG	ARG- 270	3.9	0	Hydrophobic	false
O01	NH1	ARG- 270	2.92	150.78	H-Bond (Protein Donor)	false
C10	CB	SER- 271	3.79	0	Hydrophobic	false
C03	CB	SER- 274	4.45	0	Hydrophobic	false
O02	OG	SER- 274	3.02	166.92	H-Bond (Ligand Donor)	false
C14	CZ2	TRP- 282	4.23	0	Hydrophobic	false
C11	CE3	TRP- 282	4.3	0	Hydrophobic	false
C09	CD2	TRP- 282	3.45	0	Hydrophobic	false
C04	SG	CYS- 284	3.85	0	Hydrophobic	false
C11	CB	TYR- 291	4.39	0	Hydrophobic	false
C21	CG1	VAL- 296	3.78	0	Hydrophobic	false
C12	CG2	VAL- 296	3.67	0	Hydrophobic	false
C32	CB	ALA- 299	3.74	0	Hydrophobic	false
O03	NE2	HIS- 301	3.08	133.34	H-Bond (Protein Donor)	false
C14	CD2	LEU- 309	4.47	0	Hydrophobic	false
C17	CD2	LEU- 309	3.9	0	Hydrophobic	false
O03	O	HIS- 393	3.04	145.83	H-Bond (Ligand Donor)	false
C24	CB	HIS- 393	4	0	Hydrophobic	false
C30	CD1	TYR- 397	4.48	0	Hydrophobic	false
C37	CD1	TYR- 397	4.34	0	Hydrophobic	false
C26	CD1	TYR- 397	4.42	0	Hydrophobic	false
C31	CD1	LEU- 400	3.84	0	Hydrophobic	false
C36	CD2	LEU- 410	3.58	0	Hydrophobic	false
C37	CE1	PHE- 418	4.21	0	Hydrophobic	false
C26	CE1	PHE- 418	4	0	Hydrophobic	false