scPDB - 4itf entry

Protein Data Bank Entry:

PDB ID : 4itf

Resolution :2.840 Å

Experimental Method : X-ray

Deposition Date : 2013-01-18

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:	21.962
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.013	563.625

% Hydrophobic	% Polar
70.66	29.34
According to VolSite

Ligand :

HET Code:	TFY
Formula:	C30H48N4O3
Molecular weight:	512.727 g/mol
DrugBank ID:	-
Buried Surface Area:	73.1 %
Polar Surface area:	104.29 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-11.7573	-4.95751	31.8425

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
C25	CZ	TYR- 143	4.3	0	Hydrophobic	false
C26	CE2	TYR- 143	3.91	0	Hydrophobic	false
O29	OH	TYR- 143	2.83	143.99	H-Bond (Protein Donor)	false
N36	N	ASP- 144	2.97	138.5	H-Bond (Protein Donor)	false
N35	N	ASP- 144	3.31	157.19	H-Bond (Protein Donor)	false
C25	CE2	TYR- 147	4.05	0	Hydrophobic	false
C30	CZ	PHE- 150	3.95	0	Hydrophobic	false
C21	CD1	LEU- 227	3.47	0	Hydrophobic	false
C2	CD2	LEU- 230	4.24	0	Hydrophobic	false
C24	CD1	LEU- 233	4.41	0	Hydrophobic	false
C30	CD1	LEU- 233	3.5	0	Hydrophobic	false
C13	CG2	VAL- 234	3.69	0	Hydrophobic	false
C18	CG2	VAL- 234	3.78	0	Hydrophobic	false
C32	CE2	TYR- 236	3.85	0	Hydrophobic	false
O31	OG	SER- 237	3.12	161.32	H-Bond (Ligand Donor)	false
C32	CB	SER- 237	4.36	0	Hydrophobic	false
C9	CD1	ILE- 268	4.32	0	Hydrophobic	false
C15	CD1	ILE- 268	4.19	0	Hydrophobic	false
C8	CG2	ILE- 271	4.03	0	Hydrophobic	false
C9	CG	MET- 272	4.17	0	Hydrophobic	false
O31	NH1	ARG- 274	2.87	134.43	H-Bond (Protein Donor)	false
N34	NH1	ARG- 274	2.87	158.78	H-Bond (Protein Donor)	false
C27	CG	ARG- 274	4.04	0	Hydrophobic	false
C27	CB	SER- 275	4.01	0	Hydrophobic	false
O29	OG	SER- 278	2.69	152.78	H-Bond (Ligand Donor)	false
C25	CB	SER- 278	3.8	0	Hydrophobic	false
C3	CD2	TRP- 286	3.49	0	Hydrophobic	false
C2	CE3	TRP- 286	4.39	0	Hydrophobic	false
C5	CZ2	TRP- 286	4.25	0	Hydrophobic	false
C24	SG	CYS- 288	3.5	0	Hydrophobic	false
C2	CB	TYR- 295	4.16	0	Hydrophobic	false
C1	CG2	VAL- 300	3.78	0	Hydrophobic	false
C16	CG1	VAL- 300	3.74	0	Hydrophobic	false
O22	NE2	HIS- 305	2.88	169.78	H-Bond (Ligand Donor)	false
C16	CD2	LEU- 309	3.63	0	Hydrophobic	false
C16	CD2	LEU- 313	4.19	0	Hydrophobic	false
C9	CD2	LEU- 313	3.77	0	Hydrophobic	false
O22	NE2	HIS- 397	2.99	143.02	H-Bond (Protein Donor)	false
C20	CD1	TYR- 401	4.34	0	Hydrophobic	false
C21	CD1	LEU- 404	4.27	0	Hydrophobic	false
C20	CD2	LEU- 414	4.38	0	Hydrophobic	false
C20	CG1	VAL- 418	3.75	0	Hydrophobic	false
C20	CE1	PHE- 422	4.46	0	Hydrophobic	false