Chemical Components in the PDB

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NGE : Summary

Code

NGE

One-letter code

X

Molecule name

N-glycolyl-beta-neuraminic acid

Synonyms

N-glycolylneuraminic acid
sialic acid

Systematic names

ProgramVersionName
ACDLabs 10.04 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid
OpenEye OEToolkits 1.6.1 (2S,4S,5R,6R)-2,4-dihydroxy-5-(2-hydroxyethanoylamino)-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid

Formula

C11 H19 N O10

Formal charge

0

Molecular weight

325.269 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)CO)C(O)C1
SMILES CACTVS 3.352 OC[CH](O)[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1NC(=O)CO)C(O)=O
SMILES OpenEye OEToolkits 1.6.1 C1C(C(C(OC1(C(=O)O)O)C(C(CO)O)O)NC(=O)CO)O
Canonical SMILES CACTVS 3.352 OC[C@@H](O)[C@@H](O)[C@@H]1O[C@@](O)(C[C@H](O)[C@H]1NC(=O)CO)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.6.1 C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)NC(=O)CO)O

IUPAC InChI

InChI=1S/C11H19NO10/c13-2-5(16)8(18)9-7(12-6(17)3-14)4(15)1-11(21,22-9)10(19)20/h4-5,7-9,13-16,18,21H,1-3H2,(H,12,17)(H,19,20)/t4-,5+,7+,8+,9+,11-/m0/s1

IUPAC InChI key

FDJKUWYYUZCUJX-AJKRCSPLSA-N
NGE

wwPDB Information

Atom count

41 (22 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, beta linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2009-11-05

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



NGE : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O9 O O8 N N N 0 2.739 4.547 -0.186
2 C9 C C8 N N N 0 1.47 3.913 -0.368
3 C8 C C7 R N N 0 1.541 2.474 0.148
4 O8 O O7 N N N 0 1.76 2.485 1.56
5 C7 C C6 R N N 0 0.225 1.758 -0.158
6 O7 O O6 N N N 0 0.005 1.748 -1.57
7 C6 C C5 R N N 0 0.295 0.319 0.357
8 O6 O O5 N N N 0 1.44 -0.331 -0.198
9 C1 C C9 N N N 0 2.862 -2.252 -0.383
10 O1A O O9B N N N 0 3.58 -1.549 -1.055
11 O1B O O9A N N N 0 3.175 -3.544 -0.193
12 O2 O O1 N N Y 0 1.741 -1.705 1.664
13 C3 C C2 N N N 0 0.404 -2.514 -0.181
14 C4 C C3 S N N 0 -0.865 -1.89 0.408
15 O4 O O3 N N N 0 -2.009 -2.62 -0.04
16 C5 C C4 R N N 0 -0.97 -0.435 -0.059
17 N5 N N4 N N N 0 -2.141 0.194 0.557
18 C2 C C1 S N N 0 1.616 -1.679 0.241
19 C10 C C10 N N N 0 -3.355 0.065 -0.014
20 O10 O O10 N N N 0 -3.478 -0.572 -1.039
21 C11 C C11 N N N 0 -4.559 0.712 0.62
22 O11 O O11 N N N 0 -5.719 0.434 -0.167
23 HO9 H H8 N N Y 0 2.767 5.464 -0.492
24 H91 H H81C N N N 0 0.708 4.461 0.187
25 H92 H H82C N N N 0 1.215 3.907 -1.427
26 H8 H H7 N N N 0 2.362 1.952 -0.343
27 HO8 H HA N N Y 0 1.067 2.934 2.063
28 H7 H H6 N N N 0 -0.596 2.28 0.333
29 HO7 H HB N N Y 0 0.698 1.298 -2.073
30 H6 H H5 N N N 0 0.373 0.326 1.444
31 H5 H H4 N N N 0 -1.07 -0.408 -1.145
32 HO1B H H9A N N N 0 3.984 -3.866 -0.613
33 HO2 H H1 N N Y 0 2.489 -1.195 2.002
34 HO4 H HC N N Y 0 -2.006 -3.553 0.215
35 H31 H H21C N N N 0 0.516 -3.532 0.191
36 H32 H H22C N N N 0 0.332 -2.528 -1.268
37 H4 H H3 N N N 0 -0.816 -1.922 1.497
38 HN5 H HD N N N 0 -2.042 0.703 1.377
39 H111 H H111 N N N 0 -4.698 0.315 1.625
40 H112 H H112 N N N 0 -4.406 1.79 0.674
41 HO11 H H11 N N N 0 -6.533 0.821 0.183



NGE : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O9 C9 O C sing 1.43 N N
2 C9 C8 C C sing 1.53 N N
3 C8 O8 C O sing 1.43 N N
4 C8 C7 C C sing 1.53 N N
5 C7 O7 C O sing 1.43 N N
6 C7 C6 C C sing 1.53 N N
7 C6 O6 C O sing 1.43 N N
8 C6 C5 C C sing 1.53 N N
9 O6 C2 O C sing 1.43 N N
10 C1 O1A C O doub 1.21 N N
11 C1 O1B C O sing 1.34 N N
12 C1 C2 C C sing 1.51 N N
13 O2 C2 O C sing 1.43 N N
14 C3 C4 C C sing 1.53 N N
15 C3 C2 C C sing 1.53 N N
16 C4 O4 C O sing 1.43 N N
17 C4 C5 C C sing 1.53 N N
18 C5 N5 C N sing 1.47 N N
19 N5 C10 N C sing 1.35 N N
20 C10 O10 C O doub 1.21 N N
21 C10 C11 C C sing 1.51 N N
22 C11 O11 C O sing 1.43 N N
23 O9 HO9 O H sing 0.97 N N
24 C9 H91 C H sing 1.09 N N
25 C9 H92 C H sing 1.09 N N
26 C8 H8 C H sing 1.09 N N
27 O8 HO8 O H sing 0.97 N N
28 C7 H7 C H sing 1.09 N N
29 O7 HO7 O H sing 0.97 N N
30 C6 H6 C H sing 1.09 N N
31 C5 H5 C H sing 1.09 N N
32 O1B HO1B O H sing 0.97 N N
33 O2 HO2 O H sing 0.97 N N
34 C3 H31 C H sing 1.09 N N
35 C3 H32 C H sing 1.09 N N
36 C4 H4 C H sing 1.09 N N
37 O4 HO4 O H sing 0.97 N N
38 N5 HN5 N H sing 0.97 N N
39 C11 H111 C H sing 1.09 N N
40 C11 H112 C H sing 1.09 N N
41 O11 HO11 O H sing 0.97 N N



NGE : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
NGE 2wx9 Open in New Window Bound ligand 1 1
NGE 2wyk Open in New Window Bound ligand 1 1
NGE 5yyb Open in New Window Bound ligand 2 1
NGE 6s04 Open in New Window Bound ligand 2 1