scPDB - 3w0c entry

Protein Data Bank Entry:

PDB ID : 3w0c

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-10-29

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:	18.244
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.097	550.125

% Hydrophobic	% Polar
74.23	25.77
According to VolSite

Ligand :

HET Code:	6DS
Formula:	C29H33F6O5
Molecular weight:	575.560 g/mol
DrugBank ID:	-
Buried Surface Area:	80.19 %
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
10.1343	21.593	34.0009

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
C17	CE2	TYR- 143	4.17	0	Hydrophobic	false
C64	CE2	TYR- 143	3.88	0	Hydrophobic	false
C64	CE2	TYR- 147	4.38	0	Hydrophobic	false
C67	CZ	PHE- 150	3.94	0	Hydrophobic	false
F6	CD1	LEU- 227	3.33	0	Hydrophobic	false
C20	CD2	LEU- 230	3.69	0	Hydrophobic	false
C29	CB	LEU- 230	4.14	0	Hydrophobic	false
C30	CD2	LEU- 230	4.37	0	Hydrophobic	false
F6	CB	ALA- 231	3.74	0	Hydrophobic	false
C63	CD1	LEU- 233	4.16	0	Hydrophobic	false
C67	CD1	LEU- 233	4.05	0	Hydrophobic	false
C2	CG	LEU- 233	3.91	0	Hydrophobic	false
C5	CD2	LEU- 233	3.8	0	Hydrophobic	false
C3	CG2	VAL- 234	4.36	0	Hydrophobic	false
C34	CG2	VAL- 234	4.17	0	Hydrophobic	false
C29	CG2	VAL- 234	3.24	0	Hydrophobic	false
F1	CG1	VAL- 234	3.45	0	Hydrophobic	false
C17	CE2	TYR- 236	3.77	0	Hydrophobic	false
C34	CB	SER- 237	3.47	0	Hydrophobic	false
O71	OG	SER- 237	2.77	156.94	H-Bond (Protein Donor)	false
F2	CD1	ILE- 268	3.72	0	Hydrophobic	false
C14	CG2	ILE- 271	4.18	0	Hydrophobic	false
C34	CG2	ILE- 271	3.34	0	Hydrophobic	false
C14	CG	MET- 272	4.24	0	Hydrophobic	false
O2	NH2	ARG- 274	2.88	167.56	H-Bond (Protein Donor)	false
O2	NE	ARG- 274	3.46	136.24	H-Bond (Protein Donor)	false
O71	NE	ARG- 274	2.76	154.99	H-Bond (Protein Donor)	false
O2	CZ	ARG- 274	3.61	0	Ionic (Protein Cationic)	false
O71	CZ	ARG- 274	3.71	0	Ionic (Protein Cationic)	false
C14	CB	SER- 275	3.98	0	Hydrophobic	false
C6	CB	SER- 275	3.76	0	Hydrophobic	false
C10	CE2	TRP- 286	4.44	0	Hydrophobic	false
C5	CB	TRP- 286	4.17	0	Hydrophobic	false
C12	CE3	TRP- 286	3.71	0	Hydrophobic	false
C13	CZ2	TRP- 286	3.36	0	Hydrophobic	false
C63	SG	CYS- 288	4.03	0	Hydrophobic	false
C20	CB	TYR- 295	3.63	0	Hydrophobic	false
C12	CG2	VAL- 300	3.75	0	Hydrophobic	false
C9	CG1	VAL- 300	4.12	0	Hydrophobic	false
F5	CB	ALA- 303	4.05	0	Hydrophobic	false
O47	NE2	HIS- 305	2.7	173.82	H-Bond (Ligand Donor)	false
C9	CD2	LEU- 309	3.78	0	Hydrophobic	false
C26	CD2	LEU- 313	4.19	0	Hydrophobic	false
C13	CD2	LEU- 313	4.02	0	Hydrophobic	false
O47	NE2	HIS- 397	2.69	150.44	H-Bond (Protein Donor)	false
F3	CD1	TYR- 401	3.38	0	Hydrophobic	false
F4	CD1	TYR- 401	4.05	0	Hydrophobic	false
F4	CD2	LEU- 404	3.42	0	Hydrophobic	false
F4	CD2	LEU- 414	3.53	0	Hydrophobic	false
F3	CG1	VAL- 418	3.43	0	Hydrophobic	false
F3	CD1	PHE- 422	3.68	0	Hydrophobic	false
F2	CE1	PHE- 422	3.43	0	Hydrophobic	false