Chemical Components in the PDB

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GCO : Summary

Code

GCO

One-letter code

X

Molecule name

D-gluconic acid

Synonyms

GLUCONIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 D-gluconic acid
OpenEye OEToolkits 1.5.0 (2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanoic acid

Formula

C6 H12 O7

Formal charge

0

Molecular weight

196.155 Da

SMILES

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

IUPAC InChI

InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3-,4+,5-/m1/s1

IUPAC InChI key

RGHNJXZEOKUKBD-SQOUGZDYSA-N
GCO

wwPDB Information

Atom count

25 (13 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

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



GCO : Atoms of Molecule

Total Number of Atoms: 25
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 -0.362 0.157 -2.895
2 C2 C C2 R N N 0 0.321 0.635 -1.64
3 C3 C C3 S N N 0 -0.34 -0.0080 -0.421
4 C4 C C4 R N N 0 0.354 0.477 0.852
5 C5 C C5 R N N 0 -0.308 -0.166 2.072
6 C6 C C6 N N N 0 0.386 0.319 3.345
7 O1A O O11 N N N 0 0.267 -0.436 -3.738
8 O1B O O12 N N N 0 -1.671 0.39 -3.076
9 O2 O O2 N N N 0 1.702 0.269 -1.681
10 O3 O O3 N N N 0 -0.227 -1.43 -0.512
11 O4 O O4 N N N 0 1.734 0.111 0.811
12 O5 O O5 N N N 0 -1.689 0.199 2.113
13 O6 O O6 N N N 0 -0.232 -0.282 4.485
14 H2 H H2 N N N 0 0.235 1.719 -1.57
15 H3 H H3 N N N 0 -1.393 0.271 -0.389
16 H4 H H4 N N N 0 0.267 1.561 0.922
17 H5 H H5 N N N 0 -0.222 -1.25 2.002
18 H61 H H61 N N N 0 0.3 1.403 3.415
19 H62 H H62 N N N 0 1.439 0.039 3.314
20 HO1B H HO1 N N N 0 -2.111 0.083 -3.881
21 HO2 H HO2 N N N 0 1.733 -0.695 -1.743
22 HO3 H HO3 N N N 0 0.717 -1.634 -0.537
23 HO4 H HO4 N N N 0 1.766 -0.853 0.749
24 HO5 H HO5 N N N 0 -1.72 1.164 2.174
25 HO6 H HO6 N N N 0 0.234 0.049 5.264



GCO : 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 1.51 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 1.53 N N
5 C2 O2 C O sing 1.43 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 1.43 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 O1B HO1B O H sing 0.97 N N
20 O2 HO2 O H sing 0.97 N N
21 O3 HO3 O H sing 0.97 N N
22 O4 HO4 O H sing 0.97 N N
23 O5 HO5 O H sing 0.97 N N
24 O6 HO6 O H sing 0.97 N N



GCO : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
GCO 1bgg Open in New Window Bound ligand 3 1
GCO 1xlf Open in New Window Bound ligand 2 1
GCO 3o03 Open in New Window Bound ligand 1 1
GCO 3oy8 Open in New Window s 2 1
GCO 3qke Open in New Window Bound ligand 8 1
GCO 3t6c Open in New Window Bound ligand 2 1
GCO 3twb Open in New Window Bound ligand 5 1
GCO 4k2s Open in New Window Bound ligand 8 1
GCO 4zlg Open in New Window Bound ligand 1 1
GCO 6e9n Open in New Window Bound ligand 1 1
GCO 7bcp Open in New Window Bound ligand 1 1