scPDB - 3w0y entry

Protein Data Bank Entry:

PDB ID : 3w0y

Resolution :1.980 Å

Experimental Method : X-ray

Deposition Date : 2012-11-05

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_HUMAN
AC:	P11473
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.348
Number of residues:	57
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.919	621.000

% Hydrophobic	% Polar
71.20	28.80
According to VolSite

Ligand :

HET Code:	DS4
Formula:	C32H30F7O3
Molecular weight:	595.568 g/mol
DrugBank ID:	-
Buried Surface Area:	79.44 %
Polar Surface area:	60.36 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
10.7846	19.767	33.7183

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
C56	CE2	TYR- 143	3.78	0	Hydrophobic	false
O58	N	ASP- 144	2.78	170.88	H-Bond (Protein Donor)	false
C56	CD2	TYR- 147	4.04	0	Hydrophobic	false
C56	CE1	PHE- 150	3.86	0	Hydrophobic	false
F60	CE1	PHE- 150	3.5	0	Hydrophobic	false
C53	CZ	PHE- 150	3.41	0	Hydrophobic	false
F1	CD1	LEU- 227	3.2	0	Hydrophobic	false
C20	CD2	LEU- 230	3.92	0	Hydrophobic	false
C29	CB	LEU- 230	3.79	0	Hydrophobic	false
C30	CD1	LEU- 230	4.37	0	Hydrophobic	false
F3	CB	LEU- 230	4.31	0	Hydrophobic	false
F3	CB	ALA- 231	3.54	0	Hydrophobic	false
F4	CB	ALA- 231	4.39	0	Hydrophobic	false
C6	CG	LEU- 233	4.3	0	Hydrophobic	false
C20	CD2	LEU- 233	4.42	0	Hydrophobic	false
C30	CD2	LEU- 233	4.4	0	Hydrophobic	false
C34	CD2	LEU- 233	4.34	0	Hydrophobic	false
C52	CG	LEU- 233	3.89	0	Hydrophobic	false
C2	CD2	LEU- 233	3.89	0	Hydrophobic	false
F4	CB	VAL- 234	3.4	0	Hydrophobic	false
C29	CG2	VAL- 234	3.43	0	Hydrophobic	false
F6	CG1	VAL- 234	3.49	0	Hydrophobic	false
C56	CE2	TYR- 236	4.47	0	Hydrophobic	false
F60	CG	TYR- 236	4.27	0	Hydrophobic	false
F6	CD1	ILE- 268	3.49	0	Hydrophobic	false
C14	CG2	ILE- 271	4.46	0	Hydrophobic	false
C5	CG2	ILE- 271	3.76	0	Hydrophobic	false
C14	CG	MET- 272	4.02	0	Hydrophobic	false
O59	NH2	ARG- 274	2.74	151.73	H-Bond (Protein Donor)	false
O59	CZ	ARG- 274	3.58	0	Ionic (Protein Cationic)	false
C50	CB	SER- 275	4.34	0	Hydrophobic	false
C14	CB	SER- 275	3.82	0	Hydrophobic	false
C1	CB	SER- 275	3.87	0	Hydrophobic	false
C3	CB	TRP- 286	4.35	0	Hydrophobic	false
C12	CE3	TRP- 286	3.91	0	Hydrophobic	false
C13	CZ2	TRP- 286	3.61	0	Hydrophobic	false
C34	CB	TRP- 286	3.73	0	Hydrophobic	false
C34	SG	CYS- 288	3.49	0	Hydrophobic	false
C20	CB	TYR- 295	3.97	0	Hydrophobic	false
C34	CD1	TYR- 295	3.86	0	Hydrophobic	false
C20	CG2	VAL- 300	3.92	0	Hydrophobic	false
C9	CG1	VAL- 300	4.25	0	Hydrophobic	false
F1	CB	ALA- 303	3.94	0	Hydrophobic	false
O47	NE2	HIS- 305	2.73	163.44	H-Bond (Ligand Donor)	false
C9	CD2	LEU- 309	3.95	0	Hydrophobic	false
C26	CD2	LEU- 313	4.33	0	Hydrophobic	false
C13	CD2	LEU- 313	4.14	0	Hydrophobic	false
O47	NE2	HIS- 397	2.75	152.71	H-Bond (Protein Donor)	false
F5	CD1	TYR- 401	3.24	0	Hydrophobic	false
F2	CD1	TYR- 401	4.02	0	Hydrophobic	false
F2	CD2	LEU- 404	3.31	0	Hydrophobic	false
F2	CD2	LEU- 414	3.47	0	Hydrophobic	false
F3	CD2	LEU- 414	4.26	0	Hydrophobic	false
F5	CG1	VAL- 418	3.43	0	Hydrophobic	false
F5	CD1	PHE- 422	3.7	0	Hydrophobic	false
F6	CE1	PHE- 422	3.54	0	Hydrophobic	false
O59	O	HOH- 617	2.71	175.9	H-Bond (Protein Donor)	false