scPDB - 1t0i entry

Protein Data Bank Entry:

PDB ID : 1t0i

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2004-04-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)H-dependent FMN reductase LOT6
ID:	LOT6_YEAST
AC:	Q07923
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	24 %
B	76 %

Ligand binding site composition:

B-Factor:	36.733
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.134	864.000

% Hydrophobic	% Polar
47.27	52.73
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	69.49 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.3997	97.486	18.2612

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
C8M	CD	ARG- 11	3.95	0	Hydrophobic	false
O2P	NE	ARG- 11	3.15	162.72	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 11	3.04	173.79	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 11	3.88	0	Ionic (Protein Cationic)	false
C4'	CG2	VAL- 15	4.46	0	Hydrophobic	false
O1P	N	VAL- 15	3.32	122.66	H-Bond (Protein Donor)	false
O3P	N	VAL- 15	2.82	165.26	H-Bond (Protein Donor)	false
C7	CG2	ILE- 60	4.44	0	Hydrophobic	false
C8M	CD1	ILE- 60	3.36	0	Hydrophobic	false
C7M	CG	PRO- 61	4.46	0	Hydrophobic	false
C5'	CB	PRO- 93	3.85	0	Hydrophobic	false
O4	NE2	GLN- 94	3.43	175.61	H-Bond (Protein Donor)	false
C7M	CG	TYR- 95	3.84	0	Hydrophobic	false
C8M	CE2	TYR- 95	3.76	0	Hydrophobic	false
C5'	CE2	TYR- 95	3.86	0	Hydrophobic	false
C6	CB	TYR- 95	3.95	0	Hydrophobic	false
O2P	OH	TYR- 95	2.55	151.25	H-Bond (Protein Donor)	false
N5	N	ASN- 96	2.9	178.48	H-Bond (Protein Donor)	false
O4	N	TRP- 97	3.22	147.85	H-Bond (Protein Donor)	false
C7M	CB	ASP- 108	3.92	0	Hydrophobic	false
O1P	OH	TYR- 124	2.55	161.85	H-Bond (Protein Donor)	false
C4'	CE1	TYR- 124	4.44	0	Hydrophobic	false
O2	N	GLY- 126	3.06	145.09	H-Bond (Protein Donor)	false
C4'	CD1	ILE- 155	4.24	0	Hydrophobic	false
C1'	CG1	VAL- 157	4.04	0	Hydrophobic	false
C2'	CG2	VAL- 157	4.27	0	Hydrophobic	false
C3'	CG1	VAL- 157	4.28	0	Hydrophobic	false
O2'	O	HOH- 208	2.57	179.96	H-Bond (Protein Donor)	false
O2	O	HOH- 211	2.78	179.97	H-Bond (Protein Donor)	false