scPDB - 5g3s entry

Protein Data Bank Entry:

PDB ID : 5g3s

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2016-05-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavin-dependent L-tryptophan oxidase VioA
ID:	VIOA_CHRVO
AC:	Q9S3V1
Organism:	Chromobacterium violaceum
Reign:	Bacteria
TaxID:	243365
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.667
Number of residues:	63
Including
Standard Amino Acids:	61
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.137	1522.125

% Hydrophobic	% Polar
46.56	53.44
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	76.17 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
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
-32.0857	3.12802	41.0453

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
C4'	CG2	ILE- 14	4.33	0	Hydrophobic	false
O1P	N	SER- 15	3.06	165.9	H-Bond (Protein Donor)	false
O1P	OG	SER- 15	3.42	121.84	H-Bond (Protein Donor)	false
O2P	OG	SER- 15	2.56	170.78	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 38	3.27	124.76	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 38	2.61	177.02	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 38	2.77	161.59	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 38	3.48	142.26	H-Bond (Ligand Donor)	false
N3A	N	MET- 39	3.04	138.55	H-Bond (Protein Donor)	false
C2B	CG	MET- 39	4.14	0	Hydrophobic	false
O1A	NE	ARG- 46	2.88	158.07	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 46	3.47	130.6	H-Bond (Protein Donor)	false
O2A	N	ARG- 46	2.89	175.95	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 46	3.61	0	Ionic (Protein Cationic)	false
C8M	CD	ARG- 46	4.02	0	Hydrophobic	false
C9	CB	ARG- 46	4.28	0	Hydrophobic	false
C2'	CB	ARG- 46	4.48	0	Hydrophobic	false
C9A	CB	ALA- 62	4.11	0	Hydrophobic	false
C2'	CB	ALA- 62	4.14	0	Hydrophobic	false
O4	N	GLY- 63	3.32	165.16	H-Bond (Protein Donor)	false
N3	O	ARG- 64	2.9	147.69	H-Bond (Ligand Donor)	false
O4	NE	ARG- 64	2.96	126.82	H-Bond (Protein Donor)	false
O4	N	ARG- 64	3.22	149.73	H-Bond (Protein Donor)	false
N6A	O	LEU- 208	3.1	165.05	H-Bond (Ligand Donor)	false
N1A	N	LEU- 208	2.77	161.44	H-Bond (Protein Donor)	false
C1B	CG2	ILE- 241	4	0	Hydrophobic	false
C7	CD1	LEU- 267	3.58	0	Hydrophobic	false
C8	CD1	LEU- 267	3.68	0	Hydrophobic	false
C7M	CD	LYS- 269	4.33	0	Hydrophobic	false
C7M	CE1	TYR- 309	4.13	0	Hydrophobic	false
C8M	CD2	TRP- 359	3.63	0	Hydrophobic	false
O3'	OD2	ASP- 389	3.07	120.11	H-Bond (Ligand Donor)	false
N1	N	MET- 398	3.35	132.04	H-Bond (Protein Donor)	false
O2	N	MET- 398	2.74	167.12	H-Bond (Protein Donor)	false
C2'	CG	MET- 398	4.08	0	Hydrophobic	false
C4'	CG	MET- 398	4.27	0	Hydrophobic	false