scPDB - 3k9v entry

Protein Data Bank Entry:

PDB ID : 3k9v

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
ID:	CP24A_RAT
AC:	Q09128
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.492
Number of residues:	29
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.642	1869.750

% Hydrophobic	% Polar
51.44	48.56
According to VolSite

Ligand :

HET Code:	CPS
Formula:	C32H58N2O7S
Molecular weight:	614.877 g/mol
DrugBank ID:	-
Buried Surface Area:	27.88 %
Polar Surface area:	155.36 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	4
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-39.9976	-5.61508	72.4192

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
C13	CD	ARG- 128	3.94	0	Hydrophobic	false
C16	CD1	ILE- 131	4.21	0	Hydrophobic	false
C7	CH2	TRP- 134	4.18	0	Hydrophobic	false
C11	SD	MET- 148	4.3	0	Hydrophobic	false
C18	SD	MET- 148	4.08	0	Hydrophobic	false
C8	CE	MET- 246	3.47	0	Hydrophobic	false
C22	CE	MET- 246	3.54	0	Hydrophobic	false
C10	CB	ALA- 326	4.48	0	Hydrophobic	false
C21	CB	GLU- 329	3.98	0	Hydrophobic	false
N1	OE2	GLU- 329	2.84	170.71	H-Bond (Ligand Donor)	false
C4	CG2	THR- 330	4.31	0	Hydrophobic	false
C21	CG2	THR- 330	4.32	0	Hydrophobic	false
C3	CG2	VAL- 391	4.49	0	Hydrophobic	false
C12	CG1	VAL- 391	3.77	0	Hydrophobic	false
O2	O	PHE- 393	3.43	171.95	H-Bond (Ligand Donor)	false
C13	CB	THR- 394	4.03	0	Hydrophobic	false
O4	O	GLY- 499	3.07	121.34	H-Bond (Ligand Donor)	false
C21	CD1	ILE- 500	4.18	0	Hydrophobic	false