Chemical Components in the PDB

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8YV : Summary

Code

8YV

One-letter code

X

Molecule name

2-keto-D-gluconic acid

Synonyms

(3S,4R,5R)-3,4,5,6-tetrahydroxy-2-oxohexanoic acid
D-fructosonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 D-fructosonic acid
OpenEye OEToolkits 2.0.6 (3~{S},4~{R},5~{R})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexanoic acid

Formula

C6 H10 O7

Formal charge

0

Molecular weight

194.139 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(C(CO)O)(O)C(C(C(=O)O)=O)O
SMILES CACTVS 3.385 OC[CH](O)[CH](O)[CH](O)C(=O)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 C(C(C(C(C(=O)C(=O)O)O)O)O)O
Canonical SMILES CACTVS 3.385 OC[C@@H](O)[C@@H](O)[C@H](O)C(=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 C([C@H]([C@H]([C@@H](C(=O)C(=O)O)O)O)O)O

IUPAC InChI

InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-4,7-10H,1H2,(H,12,13)/t2-,3-,4+/m1/s1

IUPAC InChI key

VBUYCZFBVCCYFD-JJYYJPOSSA-N
8YV

wwPDB Information

Atom count

23 (13 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2017-03-21

Last modified at

2020-06-24

Status

Released

Obsoleted

Not Assigned



8YV : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 R N N 0 -0.573 0.077 0.32
2 C2 C C2 N N N 0 1.798 -0.494 -0.126
3 O4 O O1 N N N 0 -0.468 -0.665 1.537
4 O1A O O2 N N N 0 2.06 1.824 -0.37
5 C1 C C3 N N N 0 2.559 0.781 -0.002
6 O1B O O3 N N N 0 3.801 0.776 0.518
7 O2 O O4 N N N 0 2.296 -1.533 0.24
8 C3 C C4 S N N 0 0.408 -0.489 -0.709
9 O3 O O5 N N N 0 0.028 -1.824 -1.046
10 C5 C C5 R N N 0 -2.0 -0.033 -0.222
11 O5 O O6 N N N 0 -2.105 0.709 -1.439
12 C6 C C6 N N N 0 -2.981 0.533 0.806
13 O6 O O7 N N N 0 -4.32 0.325 0.352
14 H4 H H1 N N N 0 -0.336 1.123 0.511
15 HO4 H H2 N N N 0 -0.666 -1.607 1.441
16 HO1B H H3 N N N 0 4.255 1.628 0.578
17 H3 H H4 N N N 0 0.392 0.131 -1.605
18 HO3 H H5 N N N 0 0.02 -2.433 -0.295
19 H5 H H6 N N N 0 -2.237 -1.079 -0.413
20 HO5 H H7 N N N 0 -1.907 1.651 -1.344
21 H61 H H8 N N N 0 -2.839 0.026 1.761
22 H62 H H9 N N N 0 -2.801 1.6 0.932
23 HO6 H H10 N N N 0 -4.997 0.66 0.956



8YV : Chemical Bonds

Total Number of Bonds: 22
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C3 O C sing 1.43 N N
2 O4 C4 O C sing 1.43 N N
3 C3 C4 C C sing 1.53 N N
4 C3 C2 C C sing 1.51 N N
5 C4 C5 C C sing 1.53 N N
6 O1A C1 O C doub 1.21 N N
7 C2 C1 C C sing 1.49 N N
8 C2 O2 C O doub 1.21 N N
9 C1 O1B C O sing 1.35 N N
10 C5 C6 C C sing 1.53 N N
11 C5 O5 C O sing 1.43 N N
12 C6 O6 C O sing 1.43 N N
13 C4 H4 C H sing 1.09 N N
14 O4 HO4 O H sing 0.97 N N
15 O1B HO1B O H sing 0.97 N N
16 C3 H3 C H sing 1.09 N N
17 O3 HO3 O H sing 0.97 N N
18 C5 H5 C H sing 1.09 N N
19 O5 HO5 O H sing 0.97 N N
20 C6 H61 C H sing 1.09 N N
21 C6 H62 C H sing 1.09 N N
22 O6 HO6 O H sing 0.97 N N



8YV : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
8YV 5v7n Open in New Window Bound ligand 4 1