scPDB - 3w0i entry

Protein Data Bank Entry:

PDB ID : 3w0i

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-10-30

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:	37.502
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.131	556.875

% Hydrophobic	% Polar
72.12	27.88
According to VolSite

Ligand :

HET Code:	O11
Formula:	C26H38O5
Molecular weight:	430.577 g/mol
DrugBank ID:	-
Buried Surface Area:	67.66 %
Polar Surface area:	79.15 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
13.14	25.8945	24.6019

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
C2	CE2	TYR- 143	4.23	0	Hydrophobic	false
C1	CD2	TYR- 147	4.34	0	Hydrophobic	false
C1	CZ	PHE- 150	3.74	0	Hydrophobic	false
C23	CD2	LEU- 223	3.84	0	Hydrophobic	false
C24	CD2	LEU- 223	3.97	0	Hydrophobic	false
C25	CD2	LEU- 226	4.33	0	Hydrophobic	false
C15	CD1	LEU- 226	4.16	0	Hydrophobic	false
C19	CB	LEU- 226	4.42	0	Hydrophobic	false
C23	CB	LEU- 226	4.31	0	Hydrophobic	false
C23	CB	ALA- 227	4.26	0	Hydrophobic	false
C3	CD1	LEU- 229	4.15	0	Hydrophobic	false
C9	CG	LEU- 229	4.01	0	Hydrophobic	false
C8	CD2	LEU- 229	4.35	0	Hydrophobic	false
C4	CD2	LEU- 229	3.92	0	Hydrophobic	false
C19	CG2	VAL- 230	4.13	0	Hydrophobic	false
C22	CG2	VAL- 230	4.25	0	Hydrophobic	false
C15	CG2	VAL- 230	3.69	0	Hydrophobic	false
C1	CE2	TYR- 232	4.37	0	Hydrophobic	false
O02	OG	SER- 233	2.7	136.16	H-Bond (Protein Donor)	false
C26	CG2	ILE- 267	4.48	0	Hydrophobic	false
C9	CG2	ILE- 267	3.6	0	Hydrophobic	false
C26	CG	MET- 268	4.03	0	Hydrophobic	false
O01	NH1	ARG- 270	3.46	121.59	H-Bond (Protein Donor)	false
O02	NH1	ARG- 270	2.91	134.72	H-Bond (Protein Donor)	false
C26	CB	SER- 271	3.97	0	Hydrophobic	false
C6	CB	SER- 271	3.73	0	Hydrophobic	false
C6	CB	TRP- 282	4.36	0	Hydrophobic	false
C10	CE2	TRP- 282	4.39	0	Hydrophobic	false
C12	CZ2	TRP- 282	3.59	0	Hydrophobic	false
C11	CE3	TRP- 282	3.49	0	Hydrophobic	false
C3	SG	CYS- 284	4.42	0	Hydrophobic	false
C25	CB	TYR- 291	4	0	Hydrophobic	false
C25	CG2	VAL- 296	3.79	0	Hydrophobic	false
C17	CG1	VAL- 296	3.89	0	Hydrophobic	false
C19	CB	ALA- 299	4.27	0	Hydrophobic	false
O05	NE2	HIS- 301	3	176.13	H-Bond (Protein Donor)	false
C12	CD2	LEU- 309	4.2	0	Hydrophobic	false
C18	CD2	LEU- 309	4.18	0	Hydrophobic	false
C22	CD1	TYR- 397	4.47	0	Hydrophobic	false
C24	CD1	TYR- 397	4.07	0	Hydrophobic	false
C24	CD1	LEU- 400	4.35	0	Hydrophobic	false
C24	CD2	LEU- 410	4.06	0	Hydrophobic	false
C22	CE1	PHE- 418	4.12	0	Hydrophobic	false
O01	O	HOH- 652	2.6	151.55	H-Bond (Ligand Donor)	false
O01	O	HOH- 698	2.77	135.06	H-Bond (Protein Donor)	false