scPDB - 3dl9 entry

Protein Data Bank Entry:

PDB ID : 3dl9

Resolution :2.720 Å

Experimental Method : X-ray

Deposition Date : 2008-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vitamin D 25-hydroxylase
ID:	CP2R1_HUMAN
AC:	Q6VVX0
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	53 %
B	47 %

Ligand binding site composition:

B-Factor:	43.980
Number of residues:	17
Including
Standard Amino Acids:	17
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.832	1775.250

% Hydrophobic	% Polar
56.08	43.92
According to VolSite

Ligand :

HET Code:	BCD
Formula:	C42H70O35
Molecular weight:	1134.984 g/mol
DrugBank ID:	DB03995
Buried Surface Area:	20.38 %
Polar Surface area:	554.05 Å2

Number of
H-Bond Acceptors:	35
H-Bond Donors:	21
Rings:	9
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-24.5351	-0.775026	-12.9249

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
C64	CG	MET- 116	3.93	0	Hydrophobic	false
C25	CG	LYS- 117	4.34	0	Hydrophobic	false
C64	CG	LYS- 120	4.41	0	Hydrophobic	false
C15	CG	LYS- 120	4.4	0	Hydrophobic	false
C65	CD	LYS- 120	3.56	0	Hydrophobic	false
C33	CG	PRO- 239	4.22	0	Hydrophobic	false
C34	CB	PRO- 239	4.11	0	Hydrophobic	false
O26	O	PRO- 239	3.47	159.46	H-Bond (Ligand Donor)	false
C31	CB	PHE- 240	4.28	0	Hydrophobic	false
C32	CD1	PHE- 240	4.34	0	Hydrophobic	false
C53	CE1	PHE- 240	4.46	0	Hydrophobic	false
C54	CZ	PHE- 240	4.47	0	Hydrophobic	false
C37	CB	PHE- 240	4.23	0	Hydrophobic	false
C52	CE1	PHE- 240	4.26	0	Hydrophobic	false
C55	CE2	PHE- 240	3.99	0	Hydrophobic	false
C36	CD2	PHE- 240	3.88	0	Hydrophobic	false
O27	N	GLY- 241	3.43	150.82	H-Bond (Protein Donor)	false