scPDB - 4fhh entry

Protein Data Bank Entry:

PDB ID : 4fhh

Resolution :2.330 Å

Experimental Method : X-ray

Deposition Date : 2012-06-06

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 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:	45.079
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.170	580.500

% Hydrophobic	% Polar
77.33	22.67
According to VolSite

Ligand :

HET Code:	0U3
Formula:	C27H39NO5
Molecular weight:	457.602 g/mol
DrugBank ID:	-
Buried Surface Area:	74.49 %
Polar Surface area:	88.02 Å2

Number of
H-Bond Acceptors:	5
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
2.10955	34.4241	36.9736

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
C26	CD1	LEU- 255	4.04	0	Hydrophobic	false
C27	CD1	LEU- 255	3.65	0	Hydrophobic	false
C12	CD2	LEU- 258	4.21	0	Hydrophobic	false
C27	CB	LEU- 258	4.49	0	Hydrophobic	false
C17	CD1	LEU- 258	3.97	0	Hydrophobic	false
C27	CB	ALA- 259	4.04	0	Hydrophobic	false
C2	CD1	LEU- 261	3.69	0	Hydrophobic	false
C12	CD2	LEU- 261	4.49	0	Hydrophobic	false
C18	CD2	LEU- 261	4.29	0	Hydrophobic	false
C5	CD2	LEU- 261	3.75	0	Hydrophobic	false
C28	CG1	VAL- 262	4.11	0	Hydrophobic	false
C17	CG2	VAL- 262	3.68	0	Hydrophobic	false
C29	CG2	VAL- 262	3.91	0	Hydrophobic	false
N23	OG	SER- 265	2.58	123.35	H-Bond (Ligand Donor)	false
C11	CG2	ILE- 299	4.4	0	Hydrophobic	false
C1	CG2	ILE- 299	3.52	0	Hydrophobic	false
C11	CG	MET- 300	3.74	0	Hydrophobic	false
O22	NH1	ARG- 302	2.95	130.1	H-Bond (Protein Donor)	false
O24	NH1	ARG- 302	2.74	144.45	H-Bond (Protein Donor)	false
C20	CD	ARG- 302	4.33	0	Hydrophobic	false
C20	CB	SER- 303	4.23	0	Hydrophobic	false
C11	CB	SER- 303	3.79	0	Hydrophobic	false
C3	CB	SER- 303	3.63	0	Hydrophobic	false
C4	CB	SER- 303	3.63	0	Hydrophobic	false
C10	CZ2	TRP- 314	3.71	0	Hydrophobic	false
C33	CB	TRP- 314	4.16	0	Hydrophobic	false
C9	CE3	TRP- 314	3.8	0	Hydrophobic	false
C33	SG	CYS- 316	3.36	0	Hydrophobic	false
C12	CB	TYR- 323	3.56	0	Hydrophobic	false
C16	CG1	VAL- 328	3.64	0	Hydrophobic	false
C12	CG2	VAL- 328	3.73	0	Hydrophobic	false
C14	CG1	VAL- 328	3.63	0	Hydrophobic	false
C16	CD2	LEU- 337	3.82	0	Hydrophobic	false
C16	CD2	LEU- 338	4.39	0	Hydrophobic	false
C10	CD1	LEU- 341	4.37	0	Hydrophobic	false
C13	CD1	LEU- 341	4.22	0	Hydrophobic	false
C16	CD1	LEU- 341	4.44	0	Hydrophobic	false
O32	NE2	HIS- 423	3.25	170.43	H-Bond (Ligand Donor)	false
C26	CD1	TYR- 427	3.84	0	Hydrophobic	false
C28	CD1	TYR- 427	4.26	0	Hydrophobic	false
C26	CD2	LEU- 430	3.44	0	Hydrophobic	false
C26	CD2	LEU- 440	3.91	0	Hydrophobic	false
C28	CG1	VAL- 444	3.74	0	Hydrophobic	false
C28	CE1	PHE- 448	4.01	0	Hydrophobic	false