scPDB - 3cv9 entry

Protein Data Bank Entry:

PDB ID : 3cv9

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2008-04-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vitamin D3 dihydroxylase
ID:	CPXE_STRGO
AC:	P18326
Organism:	Streptomyces griseolus
Reign:	Bacteria
TaxID:	1909
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.041
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.161	1633.500

% Hydrophobic	% Polar
60.12	39.88
According to VolSite

Ligand :

HET Code:	VDX
Formula:	C27H44O3
Molecular weight:	416.636 g/mol
DrugBank ID:	DB00136
Buried Surface Area:	62.96 %
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
0.171633	3.8812	14.2149

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	CE1	PHE- 78	4.18	0	Hydrophobic	false
C27	CE1	PHE- 78	3.85	0	Hydrophobic	false
O3	OG1	THR- 81	2.98	169.48	H-Bond (Protein Donor)	false
C26	CB	THR- 81	4.49	0	Hydrophobic	false
C11	CB	ALA- 84	4.42	0	Hydrophobic	false
C18	CE1	PHE- 85	3.72	0	Hydrophobic	false
C11	CD1	PHE- 85	4.21	0	Hydrophobic	false
C26	CE1	PHE- 85	3.58	0	Hydrophobic	false
C4	CG2	VAL- 88	4.36	0	Hydrophobic	false
C18	CG2	VAL- 88	4.16	0	Hydrophobic	false
C9	CG2	VAL- 88	4.21	0	Hydrophobic	false
C4	CD2	LEU- 180	4.18	0	Hydrophobic	false
C9	CD1	LEU- 180	3.8	0	Hydrophobic	false
C15	CG2	VAL- 181	4.09	0	Hydrophobic	false
O2	NE	ARG- 193	2.92	149.79	H-Bond (Protein Donor)	false
O2	NH2	ARG- 193	3.08	138.76	H-Bond (Protein Donor)	false
C4	CG	ARG- 193	3.75	0	Hydrophobic	false
C2	CB	SER- 236	4.38	0	Hydrophobic	false
C2	SD	MET- 239	4.25	0	Hydrophobic	false
C4	SD	MET- 239	4.01	0	Hydrophobic	false
C1	CB	LEU- 240	4.27	0	Hydrophobic	false
O3	O	ILE- 293	3.06	154.98	H-Bond (Ligand Donor)	false
C21	CD1	ILE- 293	4.29	0	Hydrophobic	false
C23	CD1	ILE- 293	3.59	0	Hydrophobic	false
C16	CG1	ILE- 396	4.38	0	Hydrophobic	false
C21	CG1	ILE- 396	4.11	0	Hydrophobic	false