scPDB - 3kpf entry

Protein Data Bank Entry:

PDB ID : 3kpf

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2009-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Polyamine oxidase
ID:	PAO_MAIZE
AC:	O64411
Organism:	Zea mays
Reign:	Eukaryota
TaxID:	4577
EC Number:	1.5.3.14

Chains:

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

Ligand binding site composition:

B-Factor:	19.446
Number of residues:	67
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.020	563.625

% Hydrophobic	% Polar
54.49	45.51
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	84.71 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-49.848	16.6894	-12.1587

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
O1P	OG	SER- 15	2.99	148.94	H-Bond (Protein Donor)	false
O1P	N	SER- 15	2.95	161.19	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 35	2.88	174.24	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 35	3.41	125.83	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 35	2.76	152.43	H-Bond (Ligand Donor)	false
N3A	N	ALA- 36	3.11	133.36	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 43	3.68	0	Ionic (Protein Cationic)	false
O1A	NE	ARG- 43	2.85	169.61	H-Bond (Protein Donor)	false
O2A	N	ARG- 43	2.98	159.17	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 43	2.86	136.95	H-Bond (Protein Donor)	false
O3P	NE	ARG- 43	3.41	124.56	H-Bond (Protein Donor)	false
C8M	CG	ARG- 43	3.79	0	Hydrophobic	false
C9	CB	ARG- 43	4.34	0	Hydrophobic	false
C5'	CB	ARG- 43	4.24	0	Hydrophobic	false
C9A	CB	ALA- 58	4.15	0	Hydrophobic	false
C2'	CB	ALA- 58	4.37	0	Hydrophobic	false
O4	N	ASN- 59	2.95	175.65	H-Bond (Protein Donor)	false
N3	O	TRP- 60	2.84	153.06	H-Bond (Ligand Donor)	false
O4	N	TRP- 60	2.88	167.32	H-Bond (Protein Donor)	false
N6A	O	VAL- 237	2.89	158.31	H-Bond (Ligand Donor)	false
N1A	N	VAL- 237	2.9	140.1	H-Bond (Protein Donor)	false
C7M	CD2	TYR- 298	4.01	0	Hydrophobic	false
C7M	SD	MET- 300	4.22	0	Hydrophobic	false
C7M	CE2	TRP- 393	4.41	0	Hydrophobic	false
C8M	CE2	TRP- 393	3.7	0	Hydrophobic	false
C2B	CB	PHE- 398	4.4	0	Hydrophobic	false
C3B	CE2	TYR- 399	3.78	0	Hydrophobic	false
C2B	CZ	TYR- 399	3.89	0	Hydrophobic	false
C7M	CG2	THR- 402	3.62	0	Hydrophobic	false
C8	CB	THR- 402	3.54	0	Hydrophobic	false
C1'	CD2	PHE- 403	3.95	0	Hydrophobic	false
O2P	N	GLU- 430	3.02	149.03	H-Bond (Protein Donor)	false
C5'	CG	GLU- 430	3.85	0	Hydrophobic	false
N1	N	VAL- 440	3.39	123	H-Bond (Protein Donor)	false
O2	N	VAL- 440	2.62	176.86	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 440	4.09	0	Hydrophobic	false
C4'	CB	ALA- 443	3.84	0	Hydrophobic	false
O2	O	HOH- 512	2.59	179.93	H-Bond (Protein Donor)	false
O5B	O	HOH- 542	3.14	150.48	H-Bond (Protein Donor)	false