scPDB - 2cd8 entry

Protein Data Bank Entry:

PDB ID : 2cd8

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-01-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytochrome P450 monooxygenase PikC
ID:	PIKC_STRVZ
AC:	O87605
Organism:	Streptomyces venezuelae
Reign:	Bacteria
TaxID:	54571
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.713
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.244	1184.625

% Hydrophobic	% Polar
47.86	52.14
According to VolSite

Ligand :

HET Code:	PXI
Formula:	C25H44NO6
Molecular weight:	454.620 g/mol
DrugBank ID:	-
Buried Surface Area:	68.67 %
Polar Surface area:	86.5 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
8.65334	-16.1412	-10.7032

Binding mode :

What is Poseview ?

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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
C10	CD1	LEU- 88	3.64	0	Hydrophobic	false
C1	CD2	LEU- 93	3.68	0	Hydrophobic	false
C6	CD2	LEU- 93	3.97	0	Hydrophobic	false
N1	OE1	GLU- 94	2.96	131.04	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 94	2.6	149.67	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 94	2.96	0	Ionic (Ligand Cationic)	false
N1	OE2	GLU- 94	2.6	0	Ionic (Ligand Cationic)	false
C10	CZ	PHE- 178	3.82	0	Hydrophobic	false
C17	CB	PHE- 178	3.7	0	Hydrophobic	false
C20	CB	PHE- 178	4.33	0	Hydrophobic	false
C20	CG2	VAL- 179	3.67	0	Hydrophobic	false
C9	SD	MET- 191	4.32	0	Hydrophobic	false
C10	CG	MET- 191	3.66	0	Hydrophobic	false
C10	CE	MET- 194	4.01	0	Hydrophobic	false
C6	CD1	ILE- 239	3.83	0	Hydrophobic	false
C7	CG1	VAL- 242	3.7	0	Hydrophobic	false
C17	CG1	VAL- 242	3.52	0	Hydrophobic	false
C1	CB	ALA- 243	4.06	0	Hydrophobic	false
C24	CG2	THR- 247	3.83	0	Hydrophobic	false
C3	CG2	THR- 247	3.79	0	Hydrophobic	false
C2	CG2	VAL- 290	4.2	0	Hydrophobic	false
C24	CG2	VAL- 290	4.16	0	Hydrophobic	false
C25	CG1	VAL- 290	3.59	0	Hydrophobic	false
C25	CG2	THR- 294	4.13	0	Hydrophobic	false
C2	CG2	THR- 294	4	0	Hydrophobic	false
C5	CG2	THR- 294	4.23	0	Hydrophobic	false
C25	CE	MET- 394	3.97	0	Hydrophobic	false
C19	CD1	ILE- 395	3.6	0	Hydrophobic	false