scPDB - 2vzm entry

Protein Data Bank Entry:

PDB ID : 2vzm

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2008-08-01

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:	22.808
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.725	1245.375

% Hydrophobic	% Polar
60.70	39.30
According to VolSite

Ligand :

HET Code:	NRB
Formula:	C28H48NO7
Molecular weight:	510.683 g/mol
DrugBank ID:	-
Buried Surface Area:	68.69 %
Polar Surface area:	103.57 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
20.2149	12.889	12.8228

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	CD1	LEU- 88	4.02	0	Hydrophobic	false
C1	CD2	LEU- 93	3.71	0	Hydrophobic	false
C5	CD2	LEU- 93	3.7	0	Hydrophobic	false
N1	OE2	GLU- 94	2.77	149.93	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 94	3.01	142.72	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 94	2.77	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 94	3.01	0	Ionic (Ligand Cationic)	false
C13	CE1	PHE- 178	4.19	0	Hydrophobic	false
C20	CB	PHE- 178	3.47	0	Hydrophobic	false
C13	CG	MET- 191	3.71	0	Hydrophobic	false
C5	CD1	ILE- 239	3.88	0	Hydrophobic	false
C6	CG1	ILE- 239	3.91	0	Hydrophobic	false
C9	CD1	ILE- 239	3.91	0	Hydrophobic	false
C6	CG1	VAL- 242	4.35	0	Hydrophobic	false
C9	CG1	VAL- 242	3.6	0	Hydrophobic	false
C20	CG1	VAL- 242	3.76	0	Hydrophobic	false
C1	CB	ALA- 243	3.92	0	Hydrophobic	false
C6	CB	ALA- 243	3.48	0	Hydrophobic	false
C27	CG2	THR- 247	3.84	0	Hydrophobic	false
C2	CG2	VAL- 290	4.44	0	Hydrophobic	false
C27	CG2	VAL- 290	4.37	0	Hydrophobic	false
C28	CG1	VAL- 290	4.03	0	Hydrophobic	false
C5	CG2	THR- 294	4.22	0	Hydrophobic	false
C28	CG2	THR- 294	4.3	0	Hydrophobic	false
C2	CG2	THR- 294	4.01	0	Hydrophobic	false
C21	SD	MET- 394	4.32	0	Hydrophobic	false
C23	SD	MET- 394	3.87	0	Hydrophobic	false
C28	CG	MET- 394	3.46	0	Hydrophobic	false
C27	CD1	ILE- 395	3.76	0	Hydrophobic	false