scPDB - 1db1 entry

Protein Data Bank Entry:

PDB ID : 1db1

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1999-11-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	10.190	10.190	10.190	0.000	10.190	1

List of CHEMBLId :

CHEMBL846

Binding Site :

Uniprot Annotation

Name:	Vitamin D3 receptor
ID:	VDR_HUMAN
AC:	P11473
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.277
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.158	590.625

% Hydrophobic	% Polar
73.71	26.29
According to VolSite

Ligand :

HET Code:	VDX
Formula:	C27H44O3
Molecular weight:	416.636 g/mol
DrugBank ID:	DB00136
Buried Surface Area:	70.28 %
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:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
11.4649	22.968	34.4619

Binding mode :

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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
O2	OH	TYR- 143	2.83	138.67	H-Bond (Protein Donor)	false
C2	CE2	TYR- 143	3.93	0	Hydrophobic	false
C3	CZ	TYR- 143	4.29	0	Hydrophobic	false
C3	CE2	TYR- 147	3.85	0	Hydrophobic	false
C4	CZ	PHE- 150	4.18	0	Hydrophobic	false
C3	CZ	PHE- 150	4.26	0	Hydrophobic	false
C26	CD1	LEU- 227	3.54	0	Hydrophobic	false
C11	CD2	LEU- 230	3.96	0	Hydrophobic	false
C12	CD1	LEU- 230	4.33	0	Hydrophobic	false
C4	CD1	LEU- 233	4.23	0	Hydrophobic	false
C18	CG2	VAL- 234	3.64	0	Hydrophobic	false
C24	CG2	VAL- 234	3.93	0	Hydrophobic	false
O1	OG	SER- 237	2.78	157.09	H-Bond (Ligand Donor)	false
C22	CD1	ILE- 268	4.28	0	Hydrophobic	false
C15	CG2	ILE- 271	3.89	0	Hydrophobic	false
C16	CG	MET- 272	4.22	0	Hydrophobic	false
C1	CG	ARG- 274	3.9	0	Hydrophobic	false
O1	NH1	ARG- 274	2.86	157.32	H-Bond (Protein Donor)	false
C1	CB	SER- 275	4.25	0	Hydrophobic	false
O2	OG	SER- 278	2.91	160.24	H-Bond (Ligand Donor)	false
C3	CB	SER- 278	4.26	0	Hydrophobic	false
C9	CD2	TRP- 286	3.45	0	Hydrophobic	false
C14	CZ2	TRP- 286	4.24	0	Hydrophobic	false
C4	SG	CYS- 288	3.62	0	Hydrophobic	false
C11	CB	TYR- 295	3.96	0	Hydrophobic	false
C21	CG1	VAL- 300	4.29	0	Hydrophobic	false
C12	CG2	VAL- 300	3.92	0	Hydrophobic	false
O3	NE2	HIS- 305	2.81	158.03	H-Bond (Protein Donor)	false
C21	CD2	LEU- 309	3.81	0	Hydrophobic	false
C21	CD1	LEU- 313	4.27	0	Hydrophobic	false
C17	CD1	LEU- 313	4.05	0	Hydrophobic	false
O3	NE2	HIS- 397	2.82	156.49	H-Bond (Ligand Donor)	false
C27	CD1	TYR- 401	4.36	0	Hydrophobic	false
C27	CG1	VAL- 418	3.99	0	Hydrophobic	false
C27	CE1	PHE- 422	4.34	0	Hydrophobic	false