Chemical Components in the PDB

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FO1 : Summary

Code

FO1

One-letter code

X

Molecule name

1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol

Synonyms

7,8-didemethyl-8-hydroxy-5-deazariboflavin

Systematic names

ProgramVersionName
ACDLabs 10.04 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol
OpenEye OEToolkits 1.5.0 8-hydroxy-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]pyrimido[6,5-b]quinoline-2,4-dione

Formula

C16 H17 N3 O7

Formal charge

0

Molecular weight

363.322 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C=3C(=NC(=O)N1)N(c2c(ccc(O)c2)C=3)CC(O)C(O)C(O)CO
SMILES CACTVS 3.341 OC[CH](O)[CH](O)[CH](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13
SMILES OpenEye OEToolkits 1.5.0 c1cc2c(cc1O)N(C3=NC(=O)NC(=O)C3=C2)CC(C(C(CO)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@@H](O)[C@@H](O)[C@@H](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc2c(cc1O)N(C3=NC(=O)NC(=O)C3=C2)C[C@@H]([C@@H]([C@@H](CO)O)O)O

IUPAC InChI

InChI=1S/C16H17N3O7/c20-6-12(23)13(24)11(22)5-19-10-4-8(21)2-1-7(10)3-9-14(19)17-16(26)18-15(9)25/h1-4,11-13,20-24H,5-6H2,(H,18,25,26)/t11-,12+,13-/m0/s1

IUPAC InChI key

AUEILLWDYUBWCM-XQQFMLRXSA-N
FO1

wwPDB Information

Atom count

43 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-02-01

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



FO1 : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 1.152 -2.143 0.533
2 C1 C C1 N N N 0 1.952 -3.169 0.263
3 O1 O O1 N N N 0 1.542 -4.292 0.5
4 N2 N N2 N N N 0 3.184 -3.044 -0.253
5 C2 C C2 N N N 0 3.703 -1.827 -0.54
6 O2 O O2 N N N 0 4.819 -1.709 -1.008
7 C3 C C3 N N N 0 2.859 -0.655 -0.261
8 C4 C C4 N N N 0 3.283 0.636 -0.512
9 C5 C C5 N Y N 0 2.412 1.708 -0.216
10 C6 C C6 N Y N 0 2.817 3.032 -0.462
11 C7 C C7 N Y N 0 1.976 4.064 -0.175
12 C9 C C9 N Y N 0 0.711 3.819 0.363
13 O10 O O10 N N N 0 -0.113 4.859 0.643
14 C11 C C11 N Y N 0 0.292 2.524 0.612
15 C12 C C12 N Y N 0 1.134 1.456 0.327
16 N3 N N3 N N N 0 0.713 0.166 0.577
17 C13 C C13 N N N 0 1.527 -0.891 0.303
18 C14 C C14 N N N 0 -0.618 -0.068 1.143
19 C15 C C15 S N N 0 -1.633 -0.228 0.009
20 O3 O O3 N N N 0 -1.654 0.961 -0.783
21 C16 C C16 S N N 0 -3.023 -0.472 0.599
22 O4 O O4 N N N 0 -3.002 -1.662 1.39
23 C17 C C17 R N N 0 -4.037 -0.633 -0.535
24 O5 O O5 N N N 0 -4.059 0.557 -1.327
25 C18 C C18 N N N 0 -5.428 -0.877 0.055
26 O6 O O6 N N N 0 -6.354 -1.142 -1.001
27 HN3 H HN3 N N N 0 3.711 -3.84 -0.424
28 HC6 H HC6 N N N 0 3.794 3.231 -0.877
29 HC9 H HC9 N N N 0 -0.689 2.344 1.028
30 HC82 H HC82 N N N 0 -0.69 5.113 -0.091
31 HC11 H HC11 N N N 0 -0.602 -0.975 1.747
32 HC12 H HC12 N N N 0 -0.902 0.779 1.767
33 HC2' H HC2' N N N 0 -1.349 -1.075 -0.616
34 HO2' H HO2' N N N 0 -1.899 1.757 -0.291
35 HC3' H HC3' N N N 0 -3.307 0.375 1.223
36 HO3' H HO3' N N N 0 -2.757 -2.458 0.899
37 HC4' H HC4' N N N 0 -3.754 -1.48 -1.16
38 HO4' H HO4' N N N 0 -4.304 1.352 -0.835
39 HC51 H HC51 N N N 0 -5.391 -1.733 0.729
40 HC52 H HC52 N N N 0 -5.749 0.007 0.606
41 HO5' H HO5' N N N 0 -7.258 -1.307 -0.7
42 H21 H H21 N N N 0 4.262 0.822 -0.928
43 HC7 H HC7 N N N 0 2.29 5.08 -0.365



FO1 : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C1 N C sing 1.33 N N
2 N1 C13 N C doub 1.33 N N
3 C1 O1 C O doub 1.22 N N
4 C1 N2 C N sing 1.34 N N
5 N2 C2 N C sing 1.35 N N
6 N2 HN3 N H sing 0.97 N N
7 C2 O2 C O doub 1.22 N N
8 C2 C3 C C sing 1.47 N N
9 C3 C4 C C doub 1.38 N N
10 C3 C13 C C sing 1.47 N N
11 C4 C5 C C sing 1.41 N N
12 C4 H21 C H sing 1.08 N N
13 C5 C6 C C doub 1.41 N Y
14 C5 C12 C C sing 1.41 N Y
15 C6 C7 C C sing 1.36 N Y
16 C6 HC6 C H sing 1.08 N N
17 C7 C9 C C doub 1.4 N Y
18 C7 HC7 C H sing 1.08 N N
19 C9 O10 C O sing 1.36 N N
20 C9 C11 C C sing 1.38 N Y
21 O10 HC82 O H sing 0.97 N N
22 C11 C12 C C doub 1.39 N Y
23 C11 HC9 C H sing 1.08 N N
24 C12 N3 C N sing 1.38 N N
25 N3 C13 N C sing 1.36 N N
26 N3 C14 N C sing 1.47 N N
27 C14 C15 C C sing 1.53 N N
28 C14 HC11 C H sing 1.09 N N
29 C14 HC12 C H sing 1.09 N N
30 C15 O3 C O sing 1.43 N N
31 C15 C16 C C sing 1.53 N N
32 C15 HC2' C H sing 1.09 N N
33 O3 HO2' O H sing 0.97 N N
34 C16 O4 C O sing 1.43 N N
35 C16 C17 C C sing 1.53 N N
36 C16 HC3' C H sing 1.09 N N
37 O4 HO3' O H sing 0.97 N N
38 C17 O5 C O sing 1.43 N N
39 C17 C18 C C sing 1.53 N N
40 C17 HC4' C H sing 1.09 N N
41 O5 HO4' O H sing 0.97 N N
42 C18 O6 C O sing 1.43 N N
43 C18 HC51 C H sing 1.09 N N
44 C18 HC52 C H sing 1.09 N N
45 O6 HO5' O H sing 0.97 N N



FO1 : Used in PDB Entries

Total Number of PDB Entries: 8
Ligand Code PDB Entry ID Type Total Distinct
FO1 3c3d Open in New Window Bound ligand 4 1
FO1 3c3e Open in New Window Bound ligand 4 1
FO1 3cvv Open in New Window Bound ligand 1 1
FO1 3cvw Open in New Window Bound ligand 1 1
FO1 4cdm Open in New Window Bound ligand 1 1
FO1 4cdn Open in New Window Bound ligand 2 1
FO1 6uw1 Open in New Window Bound ligand 1 1
FO1 6uw5 Open in New Window Bound ligand 1 1