Chemical Components in the PDB

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IDF : Summary

Code

IDF

One-letter code

X

Molecule name

5-fluoro-alpha-L-idopyranosyluronic acid fluoride

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S,3S,4R,5R,6S)-2,6-difluoro-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
OpenEye OEToolkits 1.7.6 (2S,3S,4R,5R,6S)-2,6-bis(fluoranyl)-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid

Formula

C6 H8 F2 O6

Formal charge

0

Molecular weight

214.121 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 FC1OC(F)(C(=O)O)C(O)C(O)C1O
SMILES CACTVS 3.370 O[CH]1[CH](F)O[C](F)([CH](O)[CH]1O)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 C1(C(C(OC(C1O)(C(=O)O)F)F)O)O
Canonical SMILES CACTVS 3.370 O[C@H]1[C@H](F)O[C@](F)([C@@H](O)[C@@H]1O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 [C@H]1([C@H]([C@@H](O[C@]([C@H]1O)(C(=O)O)F)F)O)O

IUPAC InChI

InChI=1S/C6H8F2O6/c7-4-2(10)1(9)3(11)6(8,14-4)5(12)13/h1-4,9-11H,(H,12,13)/t1-,2-,3+,4-,6-/m1/s1

IUPAC InChI key

NQKZMBDISJYOPD-ORELYVPDSA-N
IDF

wwPDB Information

Atom count

22 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-05-07

Last modified at

2013-09-13

Status

Released

Obsoleted

Not Assigned



IDF : Atoms of Molecule

Total Number of Atoms: 22
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O6B O O6B N N N 0 2.557 -0.873 1.009
2 C6 C C6 N N N 0 2.205 -0.043 0.205
3 O6A O O6A N N N 0 3.117 0.582 -0.557
4 C5 C C5 S N N 0 0.743 0.287 0.052
5 O5 O O5 N N N 0 0.056 -0.02 1.268
6 F5 F F5 N N N 0 0.599 1.649 -0.234
7 C4 C C4 S N N 0 0.149 -0.541 -1.09
8 O4 O O4 N N N 0 0.343 -1.931 -0.824
9 C3 C C3 R N N 0 -1.35 -0.245 -1.2
10 O3 O O3 N N N 0 -1.543 1.132 -1.53
11 C2 C C2 R N N 0 -2.018 -0.547 0.145
12 O2 O O2 N N N 0 -1.883 -1.938 0.444
13 C1 C C1 S N N 0 -1.341 0.281 1.24
14 F1 F F1 N N N 0 -1.52 1.643 0.974
15 H1 H H1 N N N 0 4.042 0.335 -0.426
16 H2 H H2 N N N 0 0.642 -0.277 -2.026
17 H3 H H3 N N N 0 1.271 -2.189 -0.737
18 H4 H H4 N N N 0 -1.79 -0.871 -1.976
19 H5 H H5 N N N 0 -2.471 1.39 -1.616
20 H6 H H6 N N N 0 -3.075 -0.287 0.093
21 H7 H H7 N N N 0 -2.284 -2.201 1.283
22 H8 H H8 N N N 0 -1.784 0.038 2.206



IDF : Chemical Bonds

Total Number of Bonds: 22
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F1 C1 F C sing 1.3992287 N N
2 C1 C2 C C sing 1.5306659 N N
3 C1 O5 C O sing 1.4293334 N N
4 F5 C5 F C sing 1.399134 N N
5 O2 C2 O C sing 1.4291631 N N
6 C2 C3 C C sing 1.5318136 N N
7 O5 C5 O C sing 1.4299909 N N
8 C5 C6 C C sing 1.50657 N N
9 C5 C4 C C sing 1.5305502 N N
10 O6B C6 O C doub 1.2079818 N N
11 C6 O6A C O sing 1.3427632 N N
12 C3 O3 C O sing 1.4290829 N N
13 C3 C4 C C sing 1.5318998 N N
14 C4 O4 C O sing 1.4284579 N N
15 O6A H1 O H sing 0.9663307 N N
16 C4 H2 C H sing 1.0903399 N N
17 O4 H3 O H sing 0.9671179 N N
18 C3 H4 C H sing 1.0897945 N N
19 O3 H5 O H sing 0.96702844 N N
20 C2 H6 C H sing 1.0897491 N N
21 O2 H7 O H sing 0.96638036 N N
22 C1 H8 C H sing 1.0901624 N N



IDF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
IDF 4kgj Open in New Window Bound ligand 2 1