Chemical Components in the PDB

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SKD : Summary

Code

SKD

One-letter code

X

Molecule name

2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R,2R,3S,5S,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid (non-preferred name)
OpenEye OEToolkits 1.5.0 (1S,3S,4R,5R,6R)-4-acetamido-6-[(1R)-1,2-dihydroxyethyl]-3-hydroxy-7,8-dioxabicyclo[3.2.1]octane-1-carboxylic acid

Formula

C11 H17 N O8

Formal charge

0

Molecular weight

291.255 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NC1C(O)CC2(OC1C(O2)C(O)CO)C(=O)O)C
SMILES CACTVS 3.341 CC(=O)N[CH]1[CH](O)C[C]2(O[CH]([CH](O)CO)[CH]1O2)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC1C(CC2(OC1C(O2)C(CO)O)C(=O)O)O
Canonical SMILES CACTVS 3.341 CC(=O)N[C@@H]1[C@@H](O)C[C@]2(O[C@H]([C@H](O)CO)[C@@H]1O2)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)N[C@@H]1[C@H](C[C@@]2(O[C@H]1[C@H](O2)[C@@H](CO)O)C(=O)O)O

IUPAC InChI

InChI=1S/C11H17NO8/c1-4(14)12-7-5(15)2-11(10(17)18)19-8(6(16)3-13)9(7)20-11/h5-9,13,15-16H,2-3H2,1H3,(H,12,14)(H,17,18)/t5-,6+,7+,8+,9+,11+/m0/s1

IUPAC InChI key

NCMJSVDTRDLWJE-YRMXFSIDSA-N
SKD

wwPDB Information

Atom count

37 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



SKD : Atoms of Molecule

Total Number of Atoms: 37
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 -2.791 -0.223 -0.843
2 C2 C C2 S N N 0 -1.404 0.067 -0.33
3 C3 C C3 N N N 0 -1.44 1.038 0.86
4 C4 C C4 S N N 0 -0.004 1.434 1.219
5 C5 C C5 R N N 0 0.842 0.167 1.389
6 C6 C C6 R N N 0 0.669 -0.712 0.141
7 C7 C C7 R N N 0 0.772 0.207 -1.099
8 C8 C C8 R N N 0 1.315 -0.574 -2.297
9 C9 C C9 N N N 0 1.342 0.333 -3.528
10 C10 C C10 N N N 0 0.953 -0.314 3.775
11 C11 C C11 N N N 0 0.492 -1.07 4.995
12 N5 N N5 N N N 0 0.394 -0.567 2.575
13 O1A O O1A N N N 0 -3.082 0.044 -1.984
14 O1B O O1B N N N 0 -3.703 -0.782 -0.031
15 O4 O O4 N N N 0 0.545 2.238 0.173
16 O6 O O6 N N N 0 -0.722 -1.129 0.105
17 O7 O O7 N N N 0 -0.575 0.643 -1.356
18 O8 O O8 N N N 0 2.64 -1.026 -2.009
19 O9 O O9 N N N 0 1.85 -0.396 -4.647
20 O10 O O10 N N N 0 1.826 0.521 3.874
21 H31 H 1H3 N N N 0 -1.91 0.552 1.714
22 H32 H 2H3 N N N 0 -2.007 1.929 0.587
23 H4 H H4 N N N 0 -0.004 2.0 2.15
24 H5 H H5 N N N 0 1.891 0.44 1.503
25 H6 H H6 N N N 0 1.365 -1.55 0.103
26 H7 H H7 N N N 0 1.412 1.062 -0.883
27 H8 H H8 N N N 0 0.672 -1.432 -2.492
28 H91 H 1H9 N N N 0 0.332 0.678 -3.748
29 H92 H 2H9 N N N 0 1.985 1.191 -3.333
30 H111 H 1H11 N N N 0 1.055 -0.732 5.866
31 H112 H 2H11 N N N 0 -0.569 -0.887 5.156
32 H113 H 3H11 N N N 0 0.659 -2.137 4.846
33 HN5 H HN5 N N N 0 -0.304 -1.235 2.497
34 HO9 H HO9 N N N 0 1.85 0.21 -5.4
35 HOB1 H 1HOB N N N 0 -4.593 -0.969 -0.361
36 HO4 H HO4 N N N 0 -0.015 3.022 0.099
37 HO8 H HO8 N N N 0 3.174 -0.238 -1.843



SKD : 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 C2 C C sing 1.51 N N
2 C1 O1A C O doub 1.21 N N
3 C1 O1B C O sing 1.34 N N
4 C2 C3 C C sing 1.54 N N
5 C2 O6 C O sing 1.44 N N
6 C2 O7 C O sing 1.44 N N
7 C3 C4 C C sing 1.53 N N
8 C3 H31 C H sing 1.09 N N
9 C3 H32 C H sing 1.09 N N
10 C4 C5 C C sing 1.53 N N
11 C4 O4 C O sing 1.43 N N
12 C4 H4 C H sing 1.09 N N
13 C5 C6 C C sing 1.54 N N
14 C5 N5 C N sing 1.46 N N
15 C5 H5 C H sing 1.09 N N
16 C6 C7 C C sing 1.55 N N
17 C6 O6 C O sing 1.45 N N
18 C6 H6 C H sing 1.09 N N
19 C7 C8 C C sing 1.53 N N
20 C7 O7 C O sing 1.44 N N
21 C7 H7 C H sing 1.09 N N
22 C8 C9 C C sing 1.53 N N
23 C8 O8 C O sing 1.43 N N
24 C8 H8 C H sing 1.09 N N
25 C9 O9 C O sing 1.43 N N
26 C9 H91 C H sing 1.09 N N
27 C9 H92 C H sing 1.09 N N
28 C10 C11 C C sing 1.51 N N
29 C10 N5 C N sing 1.35 N N
30 C10 O10 C O doub 1.21 N N
31 C11 H111 C H sing 1.09 N N
32 C11 H112 C H sing 1.09 N N
33 C11 H113 C H sing 1.09 N N
34 N5 HN5 N H sing 0.97 N N
35 O1B HOB1 O H sing 0.97 N N
36 O4 HO4 O H sing 0.97 N N
37 O8 HO8 O H sing 0.97 N N
38 O9 HO9 O H sing 0.97 N N



SKD : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
SKD 2jkb Open in New Window Bound ligand 1 1
SKD 2sli Open in New Window Bound ligand 1 1
SKD 3sli Open in New Window Bound ligand 1 1
SKD 4x4a Open in New Window Bound ligand 1 1