scPDB - 3w5t entry

Protein Data Bank Entry:

PDB ID : 3w5t

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2013-02-06

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:	43.388
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.203	563.625

% Hydrophobic	% Polar
78.44	21.56
According to VolSite

Ligand :

HET Code:	LHP
Formula:	C27H43O4
Molecular weight:	431.628 g/mol
DrugBank ID:	-
Buried Surface Area:	71.84 %
Polar Surface area:	66.43 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	4
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
62.3941	16.2646	-4.66174

Binding mode :

What is Poseview ?

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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
OT1	OH	TYR- 143	2.54	161.61	H-Bond (Protein Donor)	false
C2	CB	LEU- 226	4.33	0	Hydrophobic	false
C12	CD2	LEU- 226	3.79	0	Hydrophobic	false
C28	CB	ALA- 227	3.62	0	Hydrophobic	false
C21	CD2	LEU- 229	3.78	0	Hydrophobic	false
C27	CG1	VAL- 230	4.15	0	Hydrophobic	false
C28	CB	VAL- 230	4.07	0	Hydrophobic	false
C4	CG2	VAL- 230	4.3	0	Hydrophobic	false
C4	CD1	ILE- 264	4.28	0	Hydrophobic	false
C7	CD1	ILE- 264	3.79	0	Hydrophobic	false
C17	CG2	ILE- 267	4.49	0	Hydrophobic	false
C16	CG2	ILE- 267	3.45	0	Hydrophobic	false
C7	CG	MET- 268	4.31	0	Hydrophobic	false
C15	CG	MET- 268	4.07	0	Hydrophobic	false
C16	CB	SER- 271	3.57	0	Hydrophobic	false
C22	CB	SER- 271	3.36	0	Hydrophobic	false
C23	CB	SER- 274	4.43	0	Hydrophobic	false
C18	CH2	TRP- 282	3.52	0	Hydrophobic	false
C20	CD2	TRP- 282	4.29	0	Hydrophobic	false
C21	CB	TRP- 282	4.2	0	Hydrophobic	false
C23	CB	TRP- 282	4.49	0	Hydrophobic	false
C23	SG	CYS- 284	3.93	0	Hydrophobic	false
C21	CD1	TYR- 291	3.91	0	Hydrophobic	false
C18	CG1	VAL- 296	4.03	0	Hydrophobic	false
C19	CB	VAL- 296	4.22	0	Hydrophobic	false
C11	CG1	VAL- 296	3.85	0	Hydrophobic	false
C2	CB	ALA- 299	4.12	0	Hydrophobic	false
C19	CD2	LEU- 305	4.43	0	Hydrophobic	false
C6	CD2	LEU- 305	3.91	0	Hydrophobic	false
C19	CD1	ILE- 306	3.28	0	Hydrophobic	false
C8	CD2	LEU- 309	4.11	0	Hydrophobic	false
C18	CD2	LEU- 309	4.24	0	Hydrophobic	false
C19	CD2	LEU- 309	4.41	0	Hydrophobic	false
O25	NE2	HIS- 393	3.31	144.36	H-Bond (Protein Donor)	false
C28	CD2	LEU- 410	3.53	0	Hydrophobic	false
C28	CG1	VAL- 414	3.37	0	Hydrophobic	false
C27	CE1	PHE- 418	4.15	0	Hydrophobic	false
OT2	O	HOH- 609	2.84	179.98	H-Bond (Protein Donor)	false