scPDB - 3cnp entry

Protein Data Bank Entry:

PDB ID : 3cnp

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-03-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Polyamine oxidase FMS1
ID:	FMS1_YEAST
AC:	P50264
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.810
Number of residues:	26
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.471	486.000

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	SP7
Formula:	C10H25N3O
Molecular weight:	203.325 g/mol
DrugBank ID:	-
Buried Surface Area:	72.76 %
Polar Surface area:	73.34 Å2

Number of
H-Bond Acceptors:	1
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
65.9324	-23.9055	56.5263

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
CAK	CZ3	TRP- 65	3.51	0	Hydrophobic	false
NAN	O	LEU- 173	3.37	124.43	H-Bond (Ligand Donor)	false
CAC	CE2	TRP- 174	4.29	0	Hydrophobic	false
CAG	CH2	TRP- 174	4.23	0	Hydrophobic	false
CAL	CE3	TRP- 174	4.49	0	Hydrophobic	false
NAE	O	TRP- 174	2.86	135.32	H-Bond (Ligand Donor)	false
CAL	CD2	LEU- 294	4.02	0	Hydrophobic	false
CAL	CD2	LEU- 375	3.53	0	Hydrophobic	false
CAC	CE1	TYR- 450	4.49	0	Hydrophobic	false
CAB	CD1	TYR- 450	3.57	0	Hydrophobic	false
CAG	CZ	TYR- 450	3.95	0	Hydrophobic	false
CAB	SG	CYS- 488	4.1	0	Hydrophobic	false
CAG	SG	CYS- 488	4.06	0	Hydrophobic	false