scPDB - 3nt6 entry

Protein Data Bank Entry:

PDB ID : 3nt6

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-07-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FAD-dependent pyridine nucleotide-disulphide oxidoreductase
ID:	A3QAV3_SHELP
AC:	A3QAV3
Organism:	Shewanella loihica
Reign:	Bacteria
TaxID:	323850
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	47 %
B	53 %

Ligand binding site composition:

B-Factor:	31.226
Number of residues:	63
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.958	1086.750

% Hydrophobic	% Polar
43.48	56.52
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	65.79 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
42.1865	-17.09	36.5751

Binding mode :

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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
C6P	CG1	VAL- 10	3.77	0	Hydrophobic	false
CDP	CB	ALA- 14	4.25	0	Hydrophobic	false
CAP	CB	ALA- 14	4.17	0	Hydrophobic	false
CAP	CB	SER- 15	4.42	0	Hydrophobic	false
CCP	CB	ALA- 18	4.23	0	Hydrophobic	false
O7A	NH1	ARG- 19	2.84	129.09	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 19	3.96	0	Ionic (Protein Cationic)	false
O7A	NE	ARG- 22	2.59	140.66	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 22	3	136.32	H-Bond (Protein Donor)	false
O4A	NH2	ARG- 22	2.92	162.39	H-Bond (Protein Donor)	false
O4A	NH1	ARG- 22	3.4	134.91	H-Bond (Protein Donor)	false
O5A	NH1	ARG- 22	2.79	139.6	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 22	3.52	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 22	3.71	0	Ionic (Protein Cationic)	false
O4A	CZ	ARG- 22	3.61	0	Ionic (Protein Cationic)	false
O5A	CZ	ARG- 22	3.78	0	Ionic (Protein Cationic)	false
CDP	CB	SER- 39	4.5	0	Hydrophobic	false
O9P	OG	SER- 39	3.02	140.8	H-Bond (Protein Donor)	false
N4P	OD1	ASN- 42	2.78	124.57	H-Bond (Ligand Donor)	false
C2P	CB	ASN- 42	3.97	0	Hydrophobic	false
S1P	OG	SER- 43	2.65	174.56	Weak HBond PROT	false
S1P	CB	SER- 43	3.36	0	Hydrophobic	false
CDP	CG	GLN- 62	4.14	0	Hydrophobic	false
CDP	CZ	PHE- 67	4.01	0	Hydrophobic	false
C2P	CB	ALA- 321	3.6	0	Hydrophobic	false
OAP	OD1	ASN- 325	2.81	122.98	H-Bond (Ligand Donor)	false
O5P	ND2	ASN- 325	3.38	155.03	H-Bond (Protein Donor)	false
O8A	CZ	ARG- 329	3.53	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 329	3.7	0	Ionic (Protein Cationic)	false
O8A	NE	ARG- 329	2.72	151.41	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 329	2.88	167.19	H-Bond (Protein Donor)	false
S1P	CE1	TYR- 446	4.1	0	Hydrophobic	false
O1A	NZ	LYS- 454	2.67	126.99	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 454	2.67	0	Ionic (Protein Cationic)	false
O1A	NE2	GLN- 459	3.07	155.96	H-Bond (Protein Donor)	false
C2B	CB	PHE- 462	4.29	0	Hydrophobic	false
C2B	CG2	VAL- 463	4.34	0	Hydrophobic	false
O9A	ND2	ASN- 466	2.75	157.98	H-Bond (Protein Donor)	false
N6A	O	VAL- 533	2.97	153.03	H-Bond (Ligand Donor)	false
C1B	CD1	LEU- 535	3.92	0	Hydrophobic	false
C4B	CD1	LEU- 535	4.34	0	Hydrophobic	false
O4B	O	HOH- 633	2.57	165.78	H-Bond (Protein Donor)	false
N1A	O	HOH- 708	2.81	180	H-Bond (Protein Donor)	false
O2B	O	HOH- 792	3.25	179.99	H-Bond (Protein Donor)	false
C2P	C2'	FAD- 900	3.96	0	Hydrophobic	false