scPDB - 3vrv entry

Protein Data Bank Entry:

PDB ID : 3vrv

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-04-14

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:	28.700
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.866	617.625

% Hydrophobic	% Polar
71.58	28.42
According to VolSite

Ligand :

HET Code:	YSD
Formula:	C28H46O3
Molecular weight:	430.663 g/mol
DrugBank ID:	-
Buried Surface Area:	73.18 %
Polar Surface area:	60.69 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-15.0179	24.9903	-3.56416

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
CAZ	CZ	TYR- 143	4.28	0	Hydrophobic	false
CBA	CE2	TYR- 143	4.42	0	Hydrophobic	false
OAF	OH	TYR- 143	2.77	150.23	H-Bond (Protein Donor)	false
CAZ	CE2	TYR- 147	3.83	0	Hydrophobic	false
CAT	CZ	PHE- 150	4.3	0	Hydrophobic	false
CAB	CD1	LEU- 223	3.43	0	Hydrophobic	false
CAB	CB	LEU- 226	3.9	0	Hydrophobic	false
CAE	CD2	LEU- 226	4.49	0	Hydrophobic	false
CAM	CD2	LEU- 226	4.38	0	Hydrophobic	false
CAU	CD1	LEU- 229	4.19	0	Hydrophobic	false
CAT	CD2	LEU- 229	4.23	0	Hydrophobic	false
CAL	CG2	VAL- 230	3.66	0	Hydrophobic	false
CAC	CG1	VAL- 230	4.16	0	Hydrophobic	false
CAP	CG2	VAL- 230	3.9	0	Hydrophobic	false
CAE	CG2	VAL- 230	3.58	0	Hydrophobic	false
OAG	OG	SER- 233	2.73	159.3	H-Bond (Ligand Donor)	false
CAQ	CD1	ILE- 264	4.07	0	Hydrophobic	false
CAO	CG2	ILE- 267	3.97	0	Hydrophobic	false
CAU	CG2	ILE- 267	4.01	0	Hydrophobic	false
CAO	CG	MET- 268	4.48	0	Hydrophobic	false
CBA	CG	ARG- 270	3.9	0	Hydrophobic	false
OAG	NH1	ARG- 270	2.87	150.5	H-Bond (Protein Donor)	false
CAU	CB	SER- 271	3.93	0	Hydrophobic	false
CAZ	CB	SER- 274	4.21	0	Hydrophobic	false
OAF	OG	SER- 274	2.8	170.53	H-Bond (Ligand Donor)	false
CAM	CE3	TRP- 282	4.1	0	Hydrophobic	false
CAN	CD2	TRP- 282	3.35	0	Hydrophobic	false
CAT	SG	CYS- 284	3.38	0	Hydrophobic	false
CAM	CB	TYR- 291	4.17	0	Hydrophobic	false
CAD	CG1	VAL- 296	4.05	0	Hydrophobic	false
CAR	CG2	VAL- 296	3.47	0	Hydrophobic	false
CAB	CB	ALA- 299	3.78	0	Hydrophobic	false
OAH	NE2	HIS- 301	2.73	165.75	H-Bond (Ligand Donor)	false
CAD	CD2	LEU- 305	3.73	0	Hydrophobic	false
CBC	CD2	LEU- 309	4.48	0	Hydrophobic	false
OAH	NE2	HIS- 393	2.61	143.91	H-Bond (Protein Donor)	false
CAC	CD1	TYR- 397	4.13	0	Hydrophobic	false
CAC	CG1	VAL- 414	4.01	0	Hydrophobic	false
CAC	CE1	PHE- 418	3.78	0	Hydrophobic	false