Chemical Components in the PDB

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9S7 : Summary

Code

9S7

One-letter code

X

Molecule name

5-acetamido-2,6-anhydro-3,5,8-trideoxy-3-fluoro-D-threo-L-galacto-nononic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 5-(acetylamino)-2,6-anhydro-3,5,8-trideoxy-3-fluoro-D-threo-L-galacto-nononic acid
OpenEye OEToolkits 2.0.6 (3~{R},4~{R},5~{R},6~{R})-5-acetamido-6-[(1~{R})-1,3-bis(oxidanyl)propyl]-3-fluoranyl-4-oxidanyl-oxane-2-carboxylic acid

Formula

C11 H18 F N O7

Formal charge

0

Molecular weight

295.262 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C1C(F)C(C(C(O1)C(O)CCO)NC(=O)C)O
SMILES CACTVS 3.385 CC(=O)N[CH]1[CH](O)[CH](F)[CH](O[CH]1[CH](O)CCO)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 CC(=O)NC1C(C(C(OC1C(CCO)O)C(=O)O)F)O
Canonical SMILES CACTVS 3.385 CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@H](O[C@H]1[C@H](O)CCO)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CC(=O)N[C@@H]1[C@H]([C@H](C(O[C@H]1[C@@H](CCO)O)C(=O)O)F)O

IUPAC InChI

InChI=1S/C11H18FNO7/c1-4(15)13-7-8(17)6(12)10(11(18)19)20-9(7)5(16)2-3-14/h5-10,14,16-17H,2-3H2,1H3,(H,13,15)(H,18,19)/t5-,6-,7-,8+,9+,10+/m1/s1

IUPAC InChI key

MCQSBVLYLCZSNU-AIGBEWNKSA-N
9S7

wwPDB Information

Atom count

38 (20 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2017-06-07

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



9S7 : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1B O O1B N N N 0 -3.292 1.653 -0.671
2 C1 C C1 N N N 0 -2.58 2.216 0.126
3 O1A O O1A N N N 0 -2.896 3.448 0.555
4 C2 C C2 R N N 0 -1.341 1.533 0.644
5 C3 C C3 R N N 0 -0.102 2.303 0.181
6 F1 F F1 N N N 0 -0.094 2.379 -1.216
7 O6 O O6 N N N 0 -1.287 0.197 0.139
8 C6 C C6 R N N 0 -0.158 -0.553 0.593
9 C7 C C7 R N N 0 -0.22 -1.968 0.014
10 C8 C C8 N N N 0 -1.561 -2.608 0.376
11 C9 C C9 N N N 0 -1.574 -4.064 -0.094
12 O9 O O9 N N N 0 -2.827 -4.663 0.245
13 O7 O O7 N N N 0 -0.089 -1.907 -1.408
14 C5 C C5 R N N 0 1.129 0.134 0.127
15 C4 C C4 R N N 0 1.155 1.569 0.66
16 O4 O O4 N N N 0 2.317 2.241 0.169
17 N5 N N5 N N N 0 2.289 -0.601 0.639
18 C10 C C10 N N N 0 3.47 -0.527 -0.005
19 O10 O O10 N N N 0 3.574 0.147 -1.008
20 C11 C C11 N N N 0 4.663 -1.283 0.522
21 H1 H H1 N N N 0 -3.703 3.844 0.197
22 H2 H H2 N N N 0 -1.368 1.509 1.734
23 H3 H H3 N N N 0 -0.12 3.309 0.6
24 H4 H H4 N N N 0 -0.169 -0.604 1.681
25 H5 H H5 N N N 0 0.592 -2.565 0.429
26 H6 H H6 N N N 0 -1.7 -2.574 1.457
27 H7 H H7 N N N 0 -2.368 -2.062 -0.112
28 H8 H H8 N N N 0 -1.435 -4.099 -1.174
29 H9 H H9 N N N 0 -0.767 -4.611 0.394
30 H10 H H10 N N N 0 -2.906 -5.588 -0.024
31 H11 H H11 N N N 0 -0.779 -1.39 -1.844
32 H12 H H12 N N N 0 1.16 0.149 -0.963
33 H13 H H13 N N N 0 1.176 1.553 1.75
34 H14 H H14 N N N 0 2.397 3.157 0.468
35 H15 H H15 N N N 0 2.205 -1.14 1.441
36 H16 H H16 N N N 0 4.38 -1.827 1.423
37 H17 H H17 N N N 0 5.01 -1.987 -0.234
38 H18 H H18 N N N 0 5.463 -0.581 0.758



9S7 : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C11 C10 C C sing 1.51 N N
2 O9 C9 O C sing 1.43 N N
3 N5 C10 N C sing 1.35 N N
4 N5 C5 N C sing 1.47 N N
5 C10 O10 C O doub 1.21 N N
6 C8 C9 C C sing 1.53 N N
7 C8 C7 C C sing 1.53 N N
8 C7 C6 C C sing 1.53 N N
9 C7 O7 C O sing 1.43 N N
10 C6 C5 C C sing 1.53 N N
11 C6 O6 C O sing 1.43 N N
12 C4 C5 C C sing 1.53 N N
13 C4 O4 C O sing 1.43 N N
14 C4 C3 C C sing 1.53 N N
15 O6 C2 O C sing 1.43 N N
16 C3 C2 C C sing 1.53 N N
17 C3 F1 C F sing 1.4 N N
18 C2 C1 C C sing 1.51 N N
19 C1 O1B C O doub 1.21 N N
20 C1 O1A C O sing 1.34 N N
21 O1A H1 O H sing 0.97 N N
22 C2 H2 C H sing 1.09 N N
23 C3 H3 C H sing 1.09 N N
24 C6 H4 C H sing 1.09 N N
25 C7 H5 C H sing 1.09 N N
26 C8 H6 C H sing 1.09 N N
27 C8 H7 C H sing 1.09 N N
28 C9 H8 C H sing 1.09 N N
29 C9 H9 C H sing 1.09 N N
30 O9 H10 O H sing 0.97 N N
31 O7 H11 O H sing 0.97 N N
32 C5 H12 C H sing 1.09 N N
33 C4 H13 C H sing 1.09 N N
34 O4 H14 O H sing 0.97 N N
35 N5 H15 N H sing 0.97 N N
36 C11 H16 C H sing 1.09 N N
37 C11 H17 C H sing 1.09 N N
38 C11 H18 C H sing 1.09 N N



9S7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9S7 5w2w Open in New Window Bound ligand 1 1