Chemical Components in the PDB

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A6P : Summary

Code

A6P

One-letter code

X

Molecule name

6-O-phosphono-alpha-D-allopyranose

Synonyms

6-O-phosphono-alpha-D-allose
6-O-phosphono-D-allose
6-O-phosphono-allose

Systematic names

ProgramVersionName
ACDLabs 10.04 6-O-phosphono-alpha-D-allopyranose
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R,6S)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl dihydrogen phosphate

Formula

C6 H13 O9 P

Formal charge

0

Molecular weight

260.136 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC1OC(O)C(O)C(O)C1O
SMILES CACTVS 3.341 O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 O[C@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H]1[C@H]([C@H]([C@H]([C@H](O1)O)O)O)O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4-,5-,6+/m1/s1

IUPAC InChI key

NBSCHQHZLSJFNQ-UKFBFLRUSA-N
A6P

wwPDB Information

Atom count

29 (16 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, alpha linking

Type code

ATOMS

Is modified

Yes

Standard parent

AFD

Defined at

2008-06-10

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



A6P : Atoms of Molecule

Total Number of Atoms: 29
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 -2.188 1.467 -0.252
2 C2 C C2 R N N 0 -3.229 0.477 -0.78
3 C3 C C3 R N N 0 -2.961 -0.905 -0.176
4 C4 C C4 S N N 0 -1.529 -1.329 -0.516
5 C5 C C5 R N N 0 -0.554 -0.269 0.0020
6 C6 C C6 N N N 0 0.875 -0.656 -0.386
7 H1 H H1 N N N 0 -2.349 2.443 -0.712
8 H1P H H1P N N N 0 3.758 -1.235 1.636
9 H2 H H2 N N N 0 -3.158 0.419 -1.867
10 H3 H H3 N N N 0 -3.664 -1.627 -0.591
11 H3P H H3P N N N 0 5.062 1.445 0.595
12 H4 H H4 N N N 0 -1.424 -1.424 -1.597
13 H5 H H5 N N N 0 -0.63 -0.204 1.088
14 H61 H H6C1 N N N 0 1.091 -1.66 -0.021
15 H62 H H6C2 N N N 0 0.975 -0.634 -1.471
16 HO1 H HA N N Y 0 -1.688 2.195 1.57
17 HO2 H HB N N Y 0 -4.773 1.787 -0.754
18 HO3 H HC N N Y 0 -4.0 -0.574 1.531
19 HO4 H HD N N Y 0 -1.827 -3.303 -0.175
20 O1 O O1 N N Y 0 -2.317 1.583 1.166
21 O1P O O1P N N N 0 3.93 -1.183 0.686
22 O2 O O2 N N N 0 -4.537 0.915 -0.409
23 O2P O O2P N N N 0 3.703 0.143 -1.451
24 O3 O O3 N N N 0 -3.117 -0.844 1.243
25 O3P O O3P N N N 0 4.099 1.441 0.678
26 O4 O O4 N N N 0 -1.243 -2.585 0.104
27 O5 O O5 N N N 0 -0.878 0.997 -0.575
28 O6 O O6 N N N 0 1.794 0.271 0.196
29 P P P N N N 0 3.388 0.167 -0.0050



A6P : Chemical Bonds

Total Number of Bonds: 29
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 C2 C3 C C sing 1.53 N N
5 C2 O2 C O sing 1.43 N N
6 C3 C4 C C sing 1.53 N N
7 C3 O3 C O sing 1.43 N N
8 C4 C5 C C sing 1.53 N N
9 C4 O4 C O sing 1.43 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 O6 P O P sing 1.61 N N
14 P O1P P O sing 1.61 N N
15 P O2P P O doub 1.48 N N
16 P O3P P O sing 1.61 N N
17 C1 H1 C H sing 1.09 N N
18 C2 H2 C H sing 1.09 N N
19 O1 HO1 O H sing 0.97 N N
20 C3 H3 C H sing 1.09 N N
21 O2 HO2 O H sing 0.97 N N
22 C4 H4 C H sing 1.09 N N
23 O3 HO3 O H sing 0.97 N N
24 C5 H5 C H sing 1.09 N N
25 O4 HO4 O H sing 0.97 N N
26 C6 H61 C H sing 1.09 N N
27 C6 H62 C H sing 1.09 N N
28 O1P H1P O H sing 0.97 N N
29 O3P H3P O H sing 0.97 N N



A6P : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
A6P 2vvo Open in New Window Bound ligand 5 1