scPDB - 4g2h entry

Protein Data Bank Entry:

PDB ID : 4g2h

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-07-12

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:	46.957
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.068	543.375

% Hydrophobic	% Polar
75.78	24.22
According to VolSite

Ligand :

HET Code:	0VQ
Formula:	C25H26F6O3
Molecular weight:	488.463 g/mol
DrugBank ID:	-
Buried Surface Area:	78.59 %
Polar Surface area:	60.69 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
2.85076	33.0436	36.8901

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
C48	CZ	TYR- 175	4.47	0	Hydrophobic	false
C52	CE2	TYR- 175	4.49	0	Hydrophobic	false
O49	OH	TYR- 175	2.73	145.77	H-Bond (Protein Donor)	false
C48	CE2	TYR- 179	3.79	0	Hydrophobic	false
C48	CZ	PHE- 182	4.48	0	Hydrophobic	false
F45	CD1	LEU- 255	3.53	0	Hydrophobic	false
F46	CB	LEU- 258	4.05	0	Hydrophobic	false
C17	CD1	LEU- 258	4.33	0	Hydrophobic	false
F46	CB	ALA- 259	4.31	0	Hydrophobic	false
C4	CD2	LEU- 261	4.24	0	Hydrophobic	false
C1	CD1	LEU- 261	4.29	0	Hydrophobic	false
C5	CD2	LEU- 261	3.7	0	Hydrophobic	false
F43	CB	VAL- 262	3.38	0	Hydrophobic	false
F42	CG1	VAL- 262	3.61	0	Hydrophobic	false
O53	OG	SER- 265	2.77	154.38	H-Bond (Ligand Donor)	false
C27	CD1	ILE- 296	4.45	0	Hydrophobic	false
C19	CD1	ILE- 296	4.41	0	Hydrophobic	false
C1	CG2	ILE- 299	3.85	0	Hydrophobic	false
C27	CE	MET- 300	4.42	0	Hydrophobic	false
C19	CG	MET- 300	3.91	0	Hydrophobic	false
C52	CD	ARG- 302	3.81	0	Hydrophobic	false
O53	NH1	ARG- 302	3	170.96	H-Bond (Protein Donor)	false
C52	CB	SER- 303	4.44	0	Hydrophobic	false
C21	CB	SER- 303	3.79	0	Hydrophobic	false
C1	CB	SER- 303	3.81	0	Hydrophobic	false
C48	CB	SER- 306	3.75	0	Hydrophobic	false
O49	OG	SER- 306	2.85	156.53	H-Bond (Ligand Donor)	false
C10	CB	TRP- 314	4.37	0	Hydrophobic	false
C4	CB	TRP- 314	4.32	0	Hydrophobic	false
C11	CD2	TRP- 314	3.64	0	Hydrophobic	false
C48	SG	CYS- 316	3.7	0	Hydrophobic	false
C10	CD1	TYR- 323	4.01	0	Hydrophobic	false
C28	CG1	VAL- 328	3.62	0	Hydrophobic	false
F47	CB	ALA- 331	3.79	0	Hydrophobic	false
O39	NE2	HIS- 333	2.81	159.24	H-Bond (Protein Donor)	false
C28	CD2	LEU- 337	3.84	0	Hydrophobic	false
C28	CD2	LEU- 338	3.77	0	Hydrophobic	false
C28	CD1	LEU- 341	3.74	0	Hydrophobic	false
C19	CD1	LEU- 341	4.16	0	Hydrophobic	false
O39	NE2	HIS- 423	2.99	155	H-Bond (Ligand Donor)	false
C40	CD1	TYR- 427	4.47	0	Hydrophobic	false
F41	CE1	TYR- 427	3.4	0	Hydrophobic	false
F45	CD1	TYR- 427	4.49	0	Hydrophobic	false
F45	CD2	LEU- 430	3.26	0	Hydrophobic	false
F41	CD2	LEU- 440	4.23	0	Hydrophobic	false
F45	CD2	LEU- 440	3.72	0	Hydrophobic	false
F41	CG1	VAL- 444	3.43	0	Hydrophobic	false
F41	CD1	PHE- 448	4.02	0	Hydrophobic	false
F42	CE1	PHE- 448	3.72	0	Hydrophobic	false