Chemical Components in the PDB

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GDL : Summary

Code

GDL

One-letter code

X

Molecule name

2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)
OpenEye OEToolkits 1.5.0 N-[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxo-oxan-3-yl]ethanamide

Formula

C8 H13 N O6

Formal charge

0

Molecular weight

219.192 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1OC(CO)C(O)C(O)C1NC(=O)C
SMILES CACTVS 3.341 CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=O
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC1C(C(C(OC1=O)CO)O)O
Canonical SMILES CACTVS 3.341 CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)OC1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](OC1=O)CO)O)O

IUPAC InChI

InChI=1S/C8H13NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-7,10,12-13H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-/m1/s1

IUPAC InChI key

NELQYZRSPDCGRQ-DBRKOABJSA-N
GDL

wwPDB Information

Atom count

28 (15 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2002-10-29

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



GDL : Atoms of Molecule

Total Number of Atoms: 28
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 1.148 -0.144 0.14
2 C2 C C2 R N N 0 -0.163 0.19 0.815
3 C3 C C3 R N N 0 -1.307 -0.317 -0.07
4 C4 C C4 S N N 0 -1.136 0.248 -1.483
5 C5 C C5 R N N 0 0.194 -0.236 -2.067
6 C6 C C6 N N N 0 0.41 0.397 -3.443
7 C7 C C7 N N N 0 0.227 0.175 3.22
8 C8 C C8 N N N 0 0.162 -0.498 4.567
9 N2 N N1 N N N 0 -0.226 -0.464 2.125
10 O1 O O1 N N N 0 2.052 -0.663 0.752
11 O3 O O3 N N N 0 -2.558 0.114 0.47
12 O4 O O4 N N N 0 -2.212 -0.199 -2.309
13 O5 O O5 N N N 0 1.273 0.156 -1.171
14 O6 O O6 N N N 0 1.652 -0.055 -3.986
15 O7 O O7 N N N 0 0.687 1.293 3.123
16 H2 H H2 N N N 0 -0.247 1.269 0.941
17 H3 H H3 N N N 0 -1.283 -1.406 -0.108
18 H4 H H4 N N N 0 -1.139 1.337 -1.441
19 H5 H H5 N N N 0 0.176 -1.321 -2.164
20 H61 H H6C1 N N N 0 -0.403 0.109 -4.108
21 H62 H H6C2 N N N 0 0.432 1.483 -3.343
22 H81 H H8C1 N N N 0 0.572 0.168 5.326
23 H82 H H8C2 N N N 0 -0.874 -0.729 4.808
24 H83 H H8C3 N N N 0 0.744 -1.419 4.541
25 HN2 H HB N N N 0 -0.594 -1.358 2.203
26 HO3 H HC N N Y 0 -2.622 -0.259 1.359
27 HO4 H HD N N N 0 -2.066 0.178 -3.188
28 HO6 H H6 N N N 0 1.749 0.366 -4.85



GDL : Chemical Bonds

Total Number of Bonds: 28
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 O1 C O doub 1.21 N N
3 C1 O5 C O sing 1.35 N N
4 C2 C3 C C sing 1.53 N N
5 C2 N2 C N sing 1.47 N N
6 C2 H2 C H sing 1.09 N N
7 C3 C4 C C sing 1.53 N N
8 C3 O3 C O sing 1.43 N N
9 C3 H3 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 1.53 N N
14 C5 O5 C O sing 1.46 N N
15 C5 H5 C H sing 1.09 N N
16 C6 O6 C O sing 1.43 N N
17 C6 H61 C H sing 1.09 N N
18 C6 H62 C H sing 1.09 N N
19 C7 C8 C C sing 1.51 N N
20 C7 N2 C N sing 1.35 N N
21 C7 O7 C O doub 1.21 N N
22 C8 H81 C H sing 1.09 N N
23 C8 H82 C H sing 1.09 N N
24 C8 H83 C H sing 1.09 N N
25 N2 HN2 N H sing 0.97 N N
26 O3 HO3 O H sing 0.97 N N
27 O4 HO4 O H sing 0.97 N N
28 O6 HO6 O H sing 0.97 N N



GDL : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
GDL 1o7a Open in New Window Bound ligand 6 1
GDL 1ur8 Open in New Window s 2 1
GDL 1ur9 Open in New Window s 2 1
GDL 2xsb Open in New Window Bound ligand 1 1
GDL 3kif Open in New Window Bound ligand 9 1
GDL 3kih Open in New Window Bound ligand 4 1