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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4g1z

2.500 Å

X-ray

2012-07-11

Interactomes:
Molecular Function:
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
A100 %


Ligand binding site composition:

B-Factor:63.518
Number of residues:46
Including
Standard Amino Acids: 46
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
2.161705.375

% Hydrophobic% Polar
75.6024.40
According to VolSite

Ligand :
4g1z_1 Structure
HET Code: 0VP
Formula: C31H40O4
Molecular weight: 476.647 g/mol
DrugBank ID: -
Buried Surface Area:72.43 %
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: 12

Mass center Coordinates

XYZ
1.7789134.023636.6663


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C48CZTYR- 1754.140Hydrophobic
C52CE2TYR- 1754.310Hydrophobic
O49OHTYR- 1752.72163.79H-Bond
(Ligand Donor)
C48CE2TYR- 1793.650Hydrophobic
C26CD1LEU- 2554.120Hydrophobic
C18CD1LEU- 2584.420Hydrophobic
C9CBLEU- 2583.760Hydrophobic
C29CBALA- 2594.080Hydrophobic
C5CD2LEU- 2613.540Hydrophobic
C17CG2VAL- 2624.180Hydrophobic
C25CG1VAL- 2624.280Hydrophobic
C29CBVAL- 2623.810Hydrophobic
C11CG2VAL- 2623.780Hydrophobic
C11CG2VAL- 2623.780Hydrophobic
C7CG2VAL- 2623.970Hydrophobic
O53OGSER- 2652.83157.57H-Bond
(Ligand Donor)
C23CD1ILE- 2963.370Hydrophobic
C23CGMET- 3003.40Hydrophobic
C52CGARG- 3023.680Hydrophobic
O53NH1ARG- 3022.87160.96H-Bond
(Protein Donor)
C4CBSER- 3033.980Hydrophobic
C10CBSER- 3033.840Hydrophobic
C48CBSER- 3063.650Hydrophobic
C10CE2TRP- 3143.960Hydrophobic
C4CBTRP- 3144.460Hydrophobic
C4SGCYS- 3163.960Hydrophobic
C48SGCYS- 3164.10Hydrophobic
C21CG2VAL- 3284.190Hydrophobic
C20CG1VAL- 3283.710Hydrophobic
C27CG1VAL- 3283.490Hydrophobic
C27CBALA- 3314.180Hydrophobic
C9CBALA- 3314.20Hydrophobic
O2NE2HIS- 3332.93168.4H-Bond
(Ligand Donor)
C27CBHIS- 3333.940Hydrophobic
C8CD1LEU- 3383.70Hydrophobic
C23CD1LEU- 3414.420Hydrophobic
C20CD1LEU- 3414.030Hydrophobic
O2NE2HIS- 4232.61151.05H-Bond
(Protein Donor)
C24CD1TYR- 4274.460Hydrophobic
C25CE1TYR- 4274.360Hydrophobic
C28CD1TYR- 4273.740Hydrophobic
C28CD2LEU- 4303.780Hydrophobic
C28CD2LEU- 4403.680Hydrophobic
C29CD2LEU- 4404.20Hydrophobic
C29CG1VAL- 4444.050Hydrophobic
C25CE1PHE- 4484.040Hydrophobic