scPDB - 2hbh entry

Protein Data Bank Entry:

PDB ID : 2hbh

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2006-06-14

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:	48.508
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.757	587.250

% Hydrophobic	% Polar
70.11	29.89
According to VolSite

Ligand :

HET Code:	XE4
Formula:	C26H34O3
Molecular weight:	394.546 g/mol
DrugBank ID:	DB08742
Buried Surface Area:	72.68 %
Polar Surface area:	60.69 Å2

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

Mass center Coordinates

X	Y	Z
2.15621	33.4637	37.3902

Binding mode :

What is Poseview ?

2D View
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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
C2	CZ	TYR- 175	4.29	0	Hydrophobic	false
C3	CE2	TYR- 175	3.97	0	Hydrophobic	false
O1	OH	TYR- 175	2.96	139.06	H-Bond (Protein Donor)	false
C2	CE2	TYR- 179	3.74	0	Hydrophobic	false
C1	CZ	PHE- 182	4.16	0	Hydrophobic	false
C24	CD1	LEU- 255	3.87	0	Hydrophobic	false
C14	CD2	LEU- 258	3.86	0	Hydrophobic	false
C1	CD1	LEU- 261	4.44	0	Hydrophobic	false
C26	CD2	LEU- 261	4.25	0	Hydrophobic	false
C14	CD2	LEU- 261	4.11	0	Hydrophobic	false
C25	CG1	VAL- 262	4.41	0	Hydrophobic	false
C26	CG2	VAL- 262	3.87	0	Hydrophobic	false
C21	CG2	VAL- 262	3.96	0	Hydrophobic	false
O2	OG	SER- 265	2.78	147.43	H-Bond (Ligand Donor)	false
C16	CG2	ILE- 299	4.03	0	Hydrophobic	false
C17	CG	MET- 300	4.33	0	Hydrophobic	false
C4	CD	ARG- 302	3.9	0	Hydrophobic	false
O2	NH1	ARG- 302	2.96	166.87	H-Bond (Protein Donor)	false
C4	CB	SER- 303	4.23	0	Hydrophobic	false
C16	CB	SER- 303	4.46	0	Hydrophobic	false
O1	OG	SER- 306	2.79	158.2	H-Bond (Ligand Donor)	false
C2	CB	SER- 306	3.99	0	Hydrophobic	false
C11	CZ2	TRP- 314	4.22	0	Hydrophobic	false
C15	CD2	TRP- 314	3.61	0	Hydrophobic	false
C1	SG	CYS- 316	3.61	0	Hydrophobic	false
C15	CB	TYR- 323	4.05	0	Hydrophobic	false
C19	CG1	VAL- 328	4.41	0	Hydrophobic	false
C13	CG2	VAL- 328	3.53	0	Hydrophobic	false
O3	NE2	HIS- 333	2.82	166.97	H-Bond (Protein Donor)	false
C17	CD1	LEU- 341	4.12	0	Hydrophobic	false
O3	NE2	HIS- 423	3.15	148.19	H-Bond (Ligand Donor)	false
C25	CD1	TYR- 427	3.96	0	Hydrophobic	false
C24	CD2	LEU- 430	3.77	0	Hydrophobic	false
C24	CD2	LEU- 440	4.5	0	Hydrophobic	false
C25	CG1	VAL- 444	4.06	0	Hydrophobic	false
C25	CE1	PHE- 448	4.22	0	Hydrophobic	false