scPDB - 3vrw entry

Protein Data Bank Entry:

PDB ID : 3vrw

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2012-04-16

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:	43.462
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.329	664.875

% Hydrophobic	% Polar
76.14	23.86
According to VolSite

Ligand :

HET Code:	YS5
Formula:	C32H54O3
Molecular weight:	486.769 g/mol
DrugBank ID:	-
Buried Surface Area:	70.47 %
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:	10

Mass center Coordinates

X	Y	Z
-15.0179	24.7644	-3.80206

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
CBB	CE2	TYR- 143	4.39	0	Hydrophobic	false
OAG	OH	TYR- 143	2.79	142.19	H-Bond (Protein Donor)	false
CBB	CE2	TYR- 147	3.92	0	Hydrophobic	false
CAV	CZ	PHE- 150	4.36	0	Hydrophobic	false
CAD	CD1	LEU- 223	3.86	0	Hydrophobic	false
CAF	CD2	LEU- 226	4.39	0	Hydrophobic	false
CAE	CD1	LEU- 226	4.16	0	Hydrophobic	false
CAD	CB	ALA- 227	4.24	0	Hydrophobic	false
CAV	CD2	LEU- 229	4.32	0	Hydrophobic	false
CAW	CD1	LEU- 229	4.01	0	Hydrophobic	false
CAF	CD2	LEU- 229	4.13	0	Hydrophobic	false
CAF	CG2	VAL- 230	3.9	0	Hydrophobic	false
CAD	CG2	VAL- 230	4.37	0	Hydrophobic	false
CAM	CG2	VAL- 230	3.83	0	Hydrophobic	false
CAC	CG1	VAL- 230	4.07	0	Hydrophobic	false
CBD	CG2	VAL- 230	3.91	0	Hydrophobic	false
CBD	CG2	VAL- 230	3.91	0	Hydrophobic	false
OAH	OG	SER- 233	2.61	156.97	H-Bond (Ligand Donor)	false
CAS	CD1	ILE- 264	4.02	0	Hydrophobic	false
CAM	CD1	ILE- 264	4.24	0	Hydrophobic	false
CAB	CG1	ILE- 264	4.43	0	Hydrophobic	false
CAW	CG2	ILE- 267	4.38	0	Hydrophobic	false
CAU	CG2	ILE- 267	3.94	0	Hydrophobic	false
CAB	CE	MET- 268	3.3	0	Hydrophobic	false
CBC	CG	ARG- 270	3.99	0	Hydrophobic	false
OAH	NH1	ARG- 270	2.89	152.33	H-Bond (Protein Donor)	false
CAW	CB	SER- 271	4.15	0	Hydrophobic	false
CBB	CB	SER- 274	4.42	0	Hydrophobic	false
OAG	OG	SER- 274	3.07	162.68	H-Bond (Ligand Donor)	false
CAQ	CD2	TRP- 282	3.4	0	Hydrophobic	false
CAP	CE3	TRP- 282	4.01	0	Hydrophobic	false
CAV	SG	CYS- 284	3.54	0	Hydrophobic	false
CAP	CB	TYR- 291	4.26	0	Hydrophobic	false
CAE	CG1	VAL- 296	4.29	0	Hydrophobic	false
CAT	CG2	VAL- 296	3.43	0	Hydrophobic	false
CAE	CB	ALA- 299	4.11	0	Hydrophobic	false
OAI	NE2	HIS- 301	2.83	158.34	H-Bond (Ligand Donor)	false
CAL	CD2	LEU- 305	3.61	0	Hydrophobic	false
CAL	CD2	LEU- 309	3.89	0	Hydrophobic	false
OAI	NE2	HIS- 393	2.73	151.06	H-Bond (Protein Donor)	false
CAN	CD1	TYR- 397	4.48	0	Hydrophobic	false
CAC	CD1	TYR- 397	4.26	0	Hydrophobic	false
CAD	CD2	LEU- 410	4.26	0	Hydrophobic	false
CAC	CE1	PHE- 418	3.74	0	Hydrophobic	false