Chemical Components in the PDB

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GCN : Summary

Code

GCN

One-letter code

X

Molecule name

2-amino-2,3-dideoxy-alpha-D-glucoyranose

Synonyms

3-DEOXY-D-GLUCOSAMINE
3-deoxy-alpha-D-glucosamine

Systematic names

ProgramVersionName
ACDLabs 10.04 2-amino-2,3-dideoxy-alpha-D-ribo-hexopyranose
OpenEye OEToolkits 1.5.0 (2S,3R,5S,6R)-3-amino-6-(hydroxymethyl)oxane-2,5-diol

Formula

C6 H13 N O4

Formal charge

0

Molecular weight

163.172 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(OC(O)C(N)C1)CO
SMILES CACTVS 3.341 N[CH]1C[CH](O)[CH](CO)O[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC(C1O)CO)O)N
Canonical SMILES CACTVS 3.341 N[C@@H]1C[C@H](O)[C@@H](CO)O[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O)N

IUPAC InChI

InChI=1S/C6H13NO4/c7-3-1-4(9)5(2-8)11-6(3)10/h3-6,8-10H,1-2,7H2/t3-,4+,5-,6+/m1/s1

IUPAC InChI key

SNDZDGQLFKEBLF-MOJAZDJTSA-N
GCN

wwPDB Information

Atom count

24 (11 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, alpha linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



GCN : Atoms of Molecule

Total Number of Atoms: 24
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 1.2 0.207 1.01
2 C2 C C2 R N N 0 -0.042 0.567 1.827
3 C3 C C3 N N N 0 -1.267 -0.11 1.203
4 C4 C C4 S N N 0 -1.331 0.263 -0.282
5 C5 C C5 R N N 0 0.0080 -0.076 -0.94
6 C6 C C6 N N N 0 -0.056 0.264 -2.43
7 N2 N N2 N N N 0 0.126 0.101 3.21
8 O1 O O1 N N Y 0 1.361 -1.212 0.999
9 O4 O O4 N N N 0 -2.378 -0.473 -0.916
10 O5 O O5 N N N 0 1.052 0.678 -0.327
11 O6 O O6 N N N 0 1.193 -0.052 -3.045
12 H1 H H1 N N N 0 2.079 0.667 1.461
13 H2 H H2 N N N 0 -0.181 1.648 1.821
14 H3 H H31 N N N 0 -1.177 -1.192 1.304
15 H32 H H32 N N N 0 -2.171 0.232 1.706
16 H4 H H4 N N N 0 -1.525 1.331 -0.38
17 H5 H H5 N N N 0 0.211 -1.14 -0.819
18 H61 H H61 N N N 0 -0.85 -0.315 -2.901
19 H62 H H62 N N N 0 -0.262 1.327 -2.551
20 HN21 H HN21 N N N 0 0.941 0.57 3.576
21 HN22 H HN22 N N Y 0 -0.665 0.447 3.731
22 HO1 H HO1 N N Y 0 2.154 -1.399 0.479
23 HO4 H HO4 N N Y 0 -3.2 -0.234 -0.466
24 HO6 H HO6 N N N 0 1.11 0.176 -3.981



GCN : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 O1 C O sing 1.43 N N
3 C1 O5 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.53 N N
6 C2 N2 C N sing 1.47 N N
7 C2 H2 C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 H3 C H sing 1.09 N N
10 C3 H32 C H sing 1.09 N N
11 C4 C5 C C sing 1.53 N N
12 C4 O4 C O sing 1.43 N N
13 C4 H4 C H sing 1.09 N N
14 C5 C6 C C sing 1.53 N N
15 C5 O5 C O sing 1.43 N N
16 C5 H5 C H sing 1.09 N N
17 C6 O6 C O sing 1.43 N N
18 C6 H61 C H sing 1.09 N N
19 C6 H62 C H sing 1.09 N N
20 N2 HN21 N H sing 1.01 N N
21 N2 HN22 N H sing 1.01 N N
22 O1 HO1 O H sing 0.97 N N
23 O4 HO4 O H sing 0.97 N N
24 O6 HO6 O H sing 0.97 N N



GCN : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
GCN 1fi1 Open in New Window s 1 1
GCN 1qff Open in New Window s 1 1
GCN 1qfg Open in New Window s 1 1
GCN 1qjq Open in New Window s 2 2
GCN 1qkc Open in New Window s 1 1
GCN 2grx Open in New Window s 4 2