scPDB - 4g1d entry

Protein Data Bank Entry:

PDB ID : 4g1d

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2012-07-10

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 A
ID:	VDRA_DANRE
AC:	Q9PTN2
Organism:	Danio rerio
Reign:	Eukaryota
TaxID:	7955
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	39.078
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.948	685.125

% Hydrophobic	% Polar
70.94	29.06
According to VolSite

Ligand :

HET Code:	0VK
Formula:	C30H38O4
Molecular weight:	462.620 g/mol
DrugBank ID:	-
Buried Surface Area:	69.88 %
Polar Surface area:	69.92 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
1.99779	34.25	36.8116

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
C48	CZ	TYR- 175	4.16	0	Hydrophobic	false
C52	CE2	TYR- 175	4.38	0	Hydrophobic	false
O49	OH	TYR- 175	2.75	163.27	H-Bond (Ligand Donor)	false
C48	CE2	TYR- 179	3.88	0	Hydrophobic	false
C28	CD1	LEU- 255	3.87	0	Hydrophobic	false
C9	CB	LEU- 258	3.85	0	Hydrophobic	false
C29	CB	ALA- 259	3.94	0	Hydrophobic	false
C10	CD2	LEU- 261	4.38	0	Hydrophobic	false
C5	CD2	LEU- 261	3.46	0	Hydrophobic	false
C17	CG2	VAL- 262	4.17	0	Hydrophobic	false
C25	CG1	VAL- 262	4.33	0	Hydrophobic	false
C29	CB	VAL- 262	3.82	0	Hydrophobic	false
C11	CG2	VAL- 262	3.78	0	Hydrophobic	false
C52	CB	SER- 265	4.41	0	Hydrophobic	false
O53	OG	SER- 265	2.69	158.98	H-Bond (Ligand Donor)	false
C23	CD1	ILE- 296	3.59	0	Hydrophobic	false
C23	CG	MET- 300	3.36	0	Hydrophobic	false
C52	CG	ARG- 302	3.7	0	Hydrophobic	false
O53	NH1	ARG- 302	2.73	149.55	H-Bond (Protein Donor)	false
C10	CB	SER- 303	3.58	0	Hydrophobic	false
C4	CB	SER- 303	3.85	0	Hydrophobic	false
C48	CB	SER- 306	3.75	0	Hydrophobic	false
C10	CE2	TRP- 314	4.02	0	Hydrophobic	false
C4	SG	CYS- 316	4.01	0	Hydrophobic	false
C48	SG	CYS- 316	4.07	0	Hydrophobic	false
C21	CG2	VAL- 328	4.26	0	Hydrophobic	false
C8	CG1	VAL- 328	3.26	0	Hydrophobic	false
C13	CB	ALA- 331	4.38	0	Hydrophobic	false
O2	NE2	HIS- 333	3.16	165.13	H-Bond (Ligand Donor)	false
C8	CD2	LEU- 338	3.55	0	Hydrophobic	false
C20	CD1	LEU- 341	3.81	0	Hydrophobic	false
O2	NE2	HIS- 423	2.81	151.56	H-Bond (Protein Donor)	false
C25	CE1	TYR- 427	4.43	0	Hydrophobic	false
C28	CD1	TYR- 427	4.01	0	Hydrophobic	false
C28	CD2	LEU- 430	3.86	0	Hydrophobic	false
C29	CD2	LEU- 440	4.1	0	Hydrophobic	false
C28	CD2	LEU- 440	3.56	0	Hydrophobic	false
C25	CG1	VAL- 444	4.06	0	Hydrophobic	false
C25	CE1	PHE- 448	4.14	0	Hydrophobic	false