Chemical Components in the PDB

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NAY : Summary

Code

NAY

One-letter code

X

Molecule name

6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-2-OXONONANOIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 5-(acetylamino)-3,4,5-trideoxy-D-manno-non-2-ulosonic acid
OpenEye OEToolkits 1.5.0 (5R,6R,7S,8R)-5-acetamido-6,7,8,9-tetrahydroxy-2-oxo-nonanoic acid

Formula

C11 H19 N O8

Formal charge

0

Molecular weight

293.27 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(=O)CCC(NC(=O)C)C(O)C(O)C(O)CO
SMILES CACTVS 3.341 CC(=O)N[CH](CCC(=O)C(O)=O)[CH](O)[CH](O)[CH](O)CO
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC(CCC(=O)C(=O)O)C(C(C(CO)O)O)O
Canonical SMILES CACTVS 3.341 CC(=O)N[C@H](CCC(=O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)N[C@H](CCC(=O)C(=O)O)[C@H]([C@@H]([C@@H](CO)O)O)O

IUPAC InChI

InChI=1S/C11H19NO8/c1-5(14)12-6(2-3-7(15)11(19)20)9(17)10(18)8(16)4-13/h6,8-10,13,16-18H,2-4H2,1H3,(H,12,14)(H,19,20)/t6-,8-,9-,10-/m1/s1

IUPAC InChI key

HWTGNSKUIIUDOU-PEBGCTIMSA-N
NAY

wwPDB Information

Atom count

39 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2000-07-17

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



NAY : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -0.339 0.264 5.068
2 O1A O O1A N N N 0 -0.649 -0.459 6.159
3 O1B O O1B N N N 0 0.136 1.373 5.191
4 C2 C C2 N N N 0 -0.58 -0.296 3.708
5 O2 O O2 N N N 0 -1.054 -1.4 3.585
6 C3 C C3 N N N 0 -0.233 0.514 2.486
7 C4 C C4 N N N 0 -0.576 -0.285 1.228
8 C5 C C5 R N N 0 -0.224 0.537 -0.011
9 N N N N N N 0 1.208 0.843 -0.003
10 C10 C C10 N N N 0 2.111 -0.157 -0.009
11 C11 C C11 N N N 0 3.585 0.157 -0.001
12 O10 O O10 N N N 0 1.737 -1.31 -0.021
13 O6 O O6 N N N 0 -1.965 -0.56 -1.277
14 C6 C C6 R N N 0 -0.567 -0.262 -1.269
15 C7 C C7 S N N 0 -0.215 0.561 -2.51
16 O7 O O7 N N N 0 -0.962 1.779 -2.501
17 C8 C C8 R N N 0 -0.558 -0.239 -3.768
18 O8 O O8 N N N 0 0.188 -1.457 -3.776
19 C9 C C9 N N N 0 -0.206 0.584 -5.008
20 O9 O O9 N N N 0 -0.527 -0.163 -6.183
21 HO1A H HO1A N N N 0 -0.493 -0.096 7.041
22 HC31 H 1HC3 N N N 0 0.832 0.742 2.492
23 HC32 H 2HC3 N N N 0 -0.803 1.443 2.493
24 HC41 H 1HC4 N N N 0 -1.642 -0.513 1.222
25 HC42 H 2HC4 N N N 0 -0.007 -1.214 1.222
26 HC5 H HC5 N N N 0 -0.794 1.467 -0.005
27 HN H HN N N N 0 1.507 1.766 0.005
28 H111 H 1H11 N N N 0 4.154 -0.771 -0.008
29 H112 H 2H11 N N N 0 3.836 0.744 -0.885
30 H113 H 3H11 N N N 0 3.829 0.727 0.894
31 HO6 H HO6 N N N 0 -2.432 0.286 -1.271
32 HC6 H HC6 N N N 0 0.002 -1.191 -1.276
33 HC7 H HC7 N N N 0 0.85 0.788 -2.504
34 HO9 H HO9 N N N 0 -0.29 0.39 -6.94
35 HO7 H HO7 N N N 0 -1.897 1.533 -2.507
36 HC8 H HC8 N N N 0 -1.624 -0.466 -3.774
37 HO8 H HO8 N N N 0 1.123 -1.211 -3.771
38 HC91 H 1HC9 N N N 0 -0.776 1.513 -5.001
39 HC92 H 2HC9 N N N 0 0.859 0.811 -5.002



NAY : 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 C1 O1A C O sing 1.35 N N
2 C1 O1B C O doub 1.21 N N
3 C1 C2 C C sing 1.49 N N
4 O1A HO1A O H sing 0.97 N N
5 C2 O2 C O doub 1.21 N N
6 C2 C3 C C sing 1.51 N N
7 C3 C4 C C sing 1.53 N N
8 C3 HC31 C H sing 1.09 N N
9 C3 HC32 C H sing 1.09 N N
10 C4 C5 C C sing 1.53 N N
11 C4 HC41 C H sing 1.09 N N
12 C4 HC42 C H sing 1.09 N N
13 C5 N C N sing 1.46 N N
14 C5 C6 C C sing 1.53 N N
15 C5 HC5 C H sing 1.09 N N
16 N C10 N C sing 1.35 N N
17 N HN N H sing 0.97 N N
18 C10 C11 C C sing 1.51 N N
19 C10 O10 C O doub 1.21 N N
20 C11 H111 C H sing 1.09 N N
21 C11 H112 C H sing 1.09 N N
22 C11 H113 C H sing 1.09 N N
23 O6 C6 O C sing 1.43 N N
24 O6 HO6 O H sing 0.97 N N
25 C6 C7 C C sing 1.53 N N
26 C6 HC6 C H sing 1.09 N N
27 C7 O7 C O sing 1.43 N N
28 C7 C8 C C sing 1.53 N N
29 C7 HC7 C H sing 1.09 N N
30 O7 HO7 O H sing 0.97 N N
31 C8 O8 C O sing 1.43 N N
32 C8 C9 C C sing 1.53 N N
33 C8 HC8 C H sing 1.09 N N
34 O8 HO8 O H sing 0.97 N N
35 C9 O9 C O sing 1.43 N N
36 C9 HC91 C H sing 1.09 N N
37 C9 HC92 C H sing 1.09 N N
38 O9 HO9 O H sing 0.97 N N



NAY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NAY 1f74 Open in New Window Bound ligand 2 1