scPDB - 2cdu entry

Protein Data Bank Entry:

PDB ID : 2cdu

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADH oxidase
ID:	Q9F1X5_LACSN
AC:	Q9F1X5
Organism:	Lactobacillus sanfranciscensis
Reign:	Bacteria
TaxID:	1625
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	8 %
B	92 %

Ligand binding site composition:

B-Factor:	25.932
Number of residues:	52
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.364	999.000

% Hydrophobic	% Polar
45.95	54.05
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	72.53 %
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
17.7607	9.31955	51.2866

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	N	ALA- 11	2.93	169.27	H-Bond (Protein Donor)	false
C8	CB	SER- 41	3.97	0	Hydrophobic	false
C9A	SG	CSX- 42	4.19	0	Hydrophobic	false
C2'	SG	CSX- 42	4.07	0	Hydrophobic	false
C7M	CD1	ILE- 44	4.22	0	Hydrophobic	false
O1A	N	SER- 115	3.11	159.31	H-Bond (Protein Donor)	false
C7M	SG	CYS- 133	4.28	0	Hydrophobic	false
O1A	NZ	LYS- 134	2.87	149.14	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 134	2.87	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 134	3.91	0	Ionic (Protein Cationic)	false
C8M	CD	LYS- 134	4.03	0	Hydrophobic	false
C6	CG1	ILE- 160	3.68	0	Hydrophobic	false
C7	CD1	ILE- 160	3.38	0	Hydrophobic	false
C7	CD1	ILE- 160	3.38	0	Hydrophobic	false
C8M	CZ	PHE- 245	3.38	0	Hydrophobic	false
O3'	OD1	ASP- 282	2.67	156.62	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 282	3.34	141.79	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 282	4.21	0	Hydrophobic	false
O2P	N	ASP- 282	2.89	160.41	H-Bond (Protein Donor)	false
N1	N	ALA- 300	3.05	171.12	H-Bond (Protein Donor)	false
O2	N	ALA- 300	3.03	124.78	H-Bond (Protein Donor)	false
C2'	CB	ALA- 300	4.08	0	Hydrophobic	false
C5'	CB	ALA- 303	4.04	0	Hydrophobic	false
N3	O	PHE- 425	2.85	166.13	H-Bond (Ligand Donor)	false
O2P	O	HOH- 2208	2.75	179.98	H-Bond (Protein Donor)	false
O1P	O	HOH- 2319	2.54	179.98	H-Bond (Protein Donor)	false
O2	O	HOH- 2349	3.04	125.14	H-Bond (Protein Donor)	false