scPDB - 3w0a entry

Protein Data Bank Entry:

PDB ID : 3w0a

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-10-25

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:	20.139
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.219	587.250

% Hydrophobic	% Polar
78.74	21.26
According to VolSite

Ligand :

HET Code:	DS5
Formula:	C29H31F6O5
Molecular weight:	573.544 g/mol
DrugBank ID:	-
Buried Surface Area:	78.97 %
Polar Surface area:	89.82 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
10.2039	21.4028	34.1282

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
C26	CE2	TYR- 143	4.01	0	Hydrophobic	false
C28	CE2	TYR- 143	4.06	0	Hydrophobic	false
C27	CZ	PHE- 150	3.85	0	Hydrophobic	false
F2	CD1	LEU- 227	3.33	0	Hydrophobic	false
C18	CB	LEU- 230	3.99	0	Hydrophobic	false
C23	CD2	LEU- 230	3.92	0	Hydrophobic	false
C19	CD2	LEU- 230	4.34	0	Hydrophobic	false
F2	CB	ALA- 231	3.8	0	Hydrophobic	false
C27	CD1	LEU- 233	4.03	0	Hydrophobic	false
C19	CD2	LEU- 233	4.49	0	Hydrophobic	false
C24	CG	LEU- 233	3.89	0	Hydrophobic	false
C25	CD1	LEU- 233	4.16	0	Hydrophobic	false
C1	CD2	LEU- 233	3.74	0	Hydrophobic	false
C24	CG2	VAL- 234	4.36	0	Hydrophobic	false
C12	CG2	VAL- 234	3.85	0	Hydrophobic	false
C18	CG2	VAL- 234	3.38	0	Hydrophobic	false
F5	CG1	VAL- 234	3.43	0	Hydrophobic	false
C28	CE2	TYR- 236	3.98	0	Hydrophobic	false
C24	CB	SER- 237	3.71	0	Hydrophobic	false
F6	CD1	ILE- 268	3.94	0	Hydrophobic	false
C21	CG2	ILE- 271	3.98	0	Hydrophobic	false
C24	CG2	ILE- 271	3.65	0	Hydrophobic	false
C21	CG	MET- 272	4.06	0	Hydrophobic	false
O5	CZ	ARG- 274	3.7	0	Ionic (Protein Cationic)	false
O4	CZ	ARG- 274	3.7	0	Ionic (Protein Cationic)	false
O5	NH2	ARG- 274	3.03	165.4	H-Bond (Protein Donor)	false
O5	NE	ARG- 274	3.48	140.94	H-Bond (Protein Donor)	false
O4	NE	ARG- 274	2.72	161.4	H-Bond (Protein Donor)	false
C21	CB	SER- 275	3.91	0	Hydrophobic	false
C6	CB	SER- 275	3.81	0	Hydrophobic	false
C7	CE2	TRP- 286	4.47	0	Hydrophobic	false
C5	CB	TRP- 286	4.19	0	Hydrophobic	false
C20	CZ2	TRP- 286	3.51	0	Hydrophobic	false
C22	CE3	TRP- 286	3.76	0	Hydrophobic	false
C25	SG	CYS- 288	4.08	0	Hydrophobic	false
C23	CB	TYR- 295	3.68	0	Hydrophobic	false
C11	CG1	VAL- 300	4.09	0	Hydrophobic	false
C23	CG2	VAL- 300	3.79	0	Hydrophobic	false
F1	CB	ALA- 303	4.18	0	Hydrophobic	false
O1	NE2	HIS- 305	2.71	159.38	H-Bond (Ligand Donor)	false
C11	CD2	LEU- 309	3.87	0	Hydrophobic	false
C9	CD1	LEU- 313	4.25	0	Hydrophobic	false
C20	CD1	LEU- 313	4.01	0	Hydrophobic	false
O1	NE2	HIS- 397	2.73	147.54	H-Bond (Protein Donor)	false
F3	CD1	TYR- 401	4.01	0	Hydrophobic	false
F4	CD1	TYR- 401	3.49	0	Hydrophobic	false
F3	CD2	LEU- 404	3.36	0	Hydrophobic	false
F3	CD2	LEU- 414	3.42	0	Hydrophobic	false
F4	CG1	VAL- 418	3.41	0	Hydrophobic	false
F4	CD1	PHE- 422	3.6	0	Hydrophobic	false
F6	CE1	PHE- 422	3.43	0	Hydrophobic	false