Chemical Components in the PDB

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GOS : Summary

Code

GOS

One-letter code

X

Molecule name

D-Glucitol-1,6-bisphosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 1,6-di-O-phosphono-D-glucitol
OpenEye OEToolkits 2.0.6 [(2~{S},3~{R},4~{R},5~{R})-2,3,4,5-tetrakis(oxidanyl)-6-phosphonooxy-hexyl] dihydrogen phosphate

Formula

C6 H16 O12 P2

Formal charge

0

Molecular weight

342.132 Da

SMILES

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

IUPAC InChI

InChI=1S/C6H16O12P2/c7-3(1-17-19(11,12)13)5(9)6(10)4(8)2-18-20(14,15)16/h3-10H,1-2H2,(H2,11,12,13)(H2,14,15,16)/t3-,4+,5-,6-/m1/s1

IUPAC InChI key

WOYYTQHMNDWRCW-JGWLITMVSA-N
GOS

wwPDB Information

Atom count

36 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-04-20

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



GOS : Atoms of Molecule

Total Number of Atoms: 36
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 3.132 -0.367 0.088
2 C2 C C2 S N N 0 1.862 0.268 -0.484
3 C3 C C3 R N N 0 0.64 -0.524 -0.016
4 C4 C C4 R N N 0 -0.635 0.181 -0.484
5 C5 C C5 R N N 0 -1.856 -0.54 0.089
6 C6 C C6 N N N 0 -3.131 0.165 -0.379
7 O1 O O1 N N N 0 4.279 0.301 -0.442
8 O11 O O2 N N N 0 6.036 0.181 1.51
9 O12 O O3 N N N 0 5.996 -1.546 -0.331
10 O13 O O4 N N N 0 6.82 0.762 -0.932
11 O2 O O5 N N N 0 1.758 1.618 -0.028
12 O3 O O6 N N N 0 0.643 -0.605 1.411
13 O4 O O7 N N N 0 -0.624 1.536 -0.028
14 O5 O O8 N N N 0 -1.866 -1.895 -0.367
15 O6 O O9 N N N 0 -4.265 -0.437 0.248
16 O61 O O10 N N N 0 -6.057 0.029 -1.467
17 O62 O O11 N N N 0 -6.8 -0.925 0.749
18 O63 O O12 N N N 0 -5.955 1.556 0.54
19 P1 P P1 N N N 0 5.787 -0.107 -0.055
20 P6 P P2 N N N 0 -5.776 0.055 -0.014
21 H12 H H1 N N N 0 3.126 -0.274 1.174
22 H11 H H2 N N N 0 3.166 -1.421 -0.186
23 H21 H H3 N N N 0 1.909 0.255 -1.573
24 H31 H H4 N N N 0 0.675 -1.529 -0.437
25 H41 H H5 N N N 0 -0.68 0.165 -1.572
26 H51 H H6 N N N 0 -1.81 -0.524 1.178
27 H61 H H7 N N N 0 -3.083 1.219 -0.108
28 H62 H H8 N N N 0 -3.221 0.071 -1.461
29 H1 H H9 N N N 0 5.917 1.107 1.763
30 H2 H H10 N N N 0 7.75 0.569 -0.75
31 H22 H H11 N N N 0 1.713 1.706 0.933
32 H32 H H12 N N N 0 0.613 0.254 1.854
33 H42 H H13 N N N 0 -0.585 1.626 0.934
34 H52 H H14 N N N 0 -1.906 -1.986 -1.329
35 H3 H H15 N N N 0 -7.73 -0.688 0.635
36 H4 H H16 N N N 0 -5.786 1.648 1.488



GOS : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O61 P6 O P doub 1.48 N N
2 O62 P6 O P sing 1.61 N N
3 P6 O63 P O sing 1.61 N N
4 P6 O6 P O sing 1.61 N N
5 O6 C6 O C sing 1.43 N N
6 C6 C5 C C sing 1.53 N N
7 O12 P1 O P doub 1.48 N N
8 O5 C5 O C sing 1.43 N N
9 O11 P1 O P sing 1.61 N N
10 C5 C4 C C sing 1.53 N N
11 O4 C4 O C sing 1.43 N N
12 C4 C3 C C sing 1.53 N N
13 P1 O1 P O sing 1.61 N N
14 P1 O13 P O sing 1.61 N N
15 O1 C1 O C sing 1.43 N N
16 C1 C2 C C sing 1.53 N N
17 C3 C2 C C sing 1.53 N N
18 C3 O3 C O sing 1.43 N N
19 C2 O2 C O sing 1.43 N N
20 C1 H12 C H sing 1.09 N N
21 C1 H11 C H sing 1.09 N N
22 C2 H21 C H sing 1.09 N N
23 C3 H31 C H sing 1.09 N N
24 C4 H41 C H sing 1.09 N N
25 C5 H51 C H sing 1.09 N N
26 C6 H61 C H sing 1.09 N N
27 C6 H62 C H sing 1.09 N N
28 O11 H1 O H sing 0.97 N N
29 O13 H2 O H sing 0.97 N N
30 O2 H22 O H sing 0.97 N N
31 O3 H32 O H sing 0.97 N N
32 O4 H42 O H sing 0.97 N N
33 O5 H52 O H sing 0.97 N N
34 O62 H3 O H sing 0.97 N N
35 O63 H4 O H sing 0.97 N N



GOS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GOS 5vje Open in New Window Bound ligand 2 1