scPDB - 5cho entry

Protein Data Bank Entry:

PDB ID : 5cho

Resolution :2.370 Å

Experimental Method : X-ray

Deposition Date : 2015-07-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavin reductase
ID:	M9QXS1_9BACT
AC:	M9QXS1
Organism:	uncultured bacterium
Reign:	Bacteria
TaxID:	77133
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	16 %
G	82 %
H	2 %

Ligand binding site composition:

B-Factor:	56.718
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.987	1373.625

% Hydrophobic	% Polar
40.54	59.46
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	60.19 %
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
235.785	-19.4258	48.6965

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
C7M	CG1	VAL- 48	3.9	0	Hydrophobic	false
O1P	NE2	HIS- 59	2.62	139.14	H-Bond (Protein Donor)	false
C2'	CE	MET- 61	4.37	0	Hydrophobic	false
C5'	CB	MET- 61	3.9	0	Hydrophobic	false
O2'	O	THR- 62	2.85	167.15	H-Bond (Ligand Donor)	false
C7	CG2	THR- 62	3.8	0	Hydrophobic	false
C8	CG2	THR- 62	3.91	0	Hydrophobic	false
C8	CG2	THR- 62	3.91	0	Hydrophobic	false
N5	N	ASN- 64	3.14	148.77	H-Bond (Protein Donor)	false
C6	CB	ASN- 64	3.77	0	Hydrophobic	false
C7M	CB	ASN- 64	4.31	0	Hydrophobic	false
O4	N	SER- 65	3.37	125.92	H-Bond (Protein Donor)	false
N3	O	CYS- 79	2.74	154.13	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 81	2.66	150.2	H-Bond (Ligand Donor)	false
O2	N	GLU- 81	2.97	165.22	H-Bond (Protein Donor)	false
C3B	CB	ASP- 83	4.39	0	Hydrophobic	false
C5B	CB	ALA- 84	4.37	0	Hydrophobic	false
C5'	CB	ALA- 84	4.48	0	Hydrophobic	false
O3P	N	ALA- 85	3.01	146.34	H-Bond (Protein Donor)	false
O2P	N	MET- 86	2.96	153.84	H-Bond (Protein Donor)	false
C8M	CB	ALA- 113	3.46	0	Hydrophobic	false
C8M	CB	TRP- 116	3.59	0	Hydrophobic	false
C1'	CZ2	TRP- 116	4.34	0	Hydrophobic	false
O4'	NH1	ARG- 117	2.83	149.36	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 117	2.87	166.62	H-Bond (Protein Donor)	false
O5'	NH1	ARG- 117	3.49	132.31	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 117	2.96	120.05	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 119	3.93	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 119	3.71	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 119	3.9	0	Ionic (Protein Cationic)	false
O2A	NH2	ARG- 119	2.77	151.32	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 119	2.9	163.75	H-Bond (Protein Donor)	false
C7M	CG	TYR- 181	3.63	0	Hydrophobic	false
C7M	CE2	PHE- 186	3.86	0	Hydrophobic	false
C8M	CZ	PHE- 186	3.59	0	Hydrophobic	false