Chemical Components in the PDB

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ALX : Summary

Code

ALX

One-letter code

X

Molecule name

2-O-phosphono-alpha-D-glucopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2-O-phosphono-alpha-D-glucopyranose
OpenEye OEToolkits 1.7.6 [(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate

Formula

C6 H13 O9 P

Formal charge

0

Molecular weight

260.136 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(OC1C(O)C(O)C(OC1O)CO)(O)O
SMILES CACTVS 3.385 OC[CH]1O[CH](O)[CH](O[P](O)(O)=O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 C(C1C(C(C(C(O1)O)OP(=O)(O)O)O)O)O
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@H](O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)OP(=O)(O)O)O)O)O

IUPAC InChI

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

IUPAC InChI key

SIUIENVKPUKAHD-DVKNGEFBSA-N

Is part of

Y45
ALX

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

GLC

Defined at

2014-09-11

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



ALX : 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 -0.559 1.385 -0.131
2 O1 O O1 N N Y 0 -0.731 1.607 -1.532
3 O2 O O2 N N N 0 1.532 0.256 -0.578
4 C2 C C2 R N N 0 0.275 0.12 0.088
5 C3 C C3 S N N 0 -0.479 -1.084 -0.484
6 C5 C C5 R N N 0 -2.607 0.142 -0.04
7 C6 C C6 N N N 0 -3.96 0.083 0.673
8 OAN O OAN N N N 0 4.135 0.515 -0.842
9 PAM P PAM N N N 0 2.944 0.196 0.193
10 OAO O OAO N N N 0 2.955 1.198 1.282
11 OAP O OAP N N N 0 3.153 -1.275 0.815
12 O3 O O3 N N N 0 0.258 -2.279 -0.219
13 C4 C C4 S N N 0 -1.856 -1.173 0.182
14 O4 O O4 N N N 0 -2.597 -2.25 -0.395
15 O6 O O6 N N N 0 -4.709 1.262 0.372
16 O5 O O5 N N N 0 -1.837 1.224 0.487
17 H1 H H1 N N N 0 -0.046 2.24 0.312
18 HO1 H H2 N N Y 0 -1.251 2.394 -1.745
19 H2 H H3 N N N 0 0.442 -0.026 1.155
20 H3 H H4 N N N 0 -0.6 -0.961 -1.56
21 H5 H H5 N N N 0 -2.766 0.294 -1.107
22 H61 H H6 N N N 0 -4.511 -0.794 0.335
23 H62 H H7 N N N 0 -3.8 0.019 1.75
24 H8 H H8 N N N 0 5.017 0.495 -0.445
25 H9 H H9 N N N 0 3.157 -1.983 0.157
26 HO3 H H10 N N Y 0 -0.162 -3.083 -0.554
27 H4 H H11 N N N 0 -1.733 -1.347 1.251
28 HO4 H H12 N N Y 0 -3.482 -2.362 -0.024
29 HO6 H H13 N N Y 0 -5.579 1.293 0.791



ALX : 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 C6 O6 C O sing 1.43 N N
2 C6 C5 C C sing 1.53 N N
3 C5 O5 C O sing 1.43 N N
4 C5 C4 C C sing 1.53 N N
5 O5 C1 O C sing 1.43 N N
6 O1 C1 O C sing 1.43 N N
7 O4 C4 O C sing 1.43 N N
8 C1 C2 C C sing 1.53 N N
9 C4 C3 C C sing 1.53 N N
10 C3 C2 C C sing 1.53 N N
11 C3 O3 C O sing 1.43 N N
12 C2 O2 C O sing 1.43 N N
13 O2 PAM O P sing 1.61 N N
14 OAO PAM O P doub 1.48 N N
15 PAM OAN P O sing 1.61 N N
16 PAM OAP P O sing 1.61 N N
17 C1 H1 C H sing 1.09 N N
18 O1 HO1 O H sing 0.97 N N
19 C2 H2 C H sing 1.09 N N
20 C3 H3 C H sing 1.09 N N
21 C5 H5 C H sing 1.09 N N
22 C6 H61 C H sing 1.09 N N
23 C6 H62 C H sing 1.09 N N
24 OAN H8 O H sing 0.97 N N
25 OAP H9 O H sing 0.97 N N
26 O3 HO3 O H sing 0.97 N N
27 C4 H4 C H sing 1.09 N N
28 O4 HO4 O H sing 0.97 N N
29 O6 HO6 O H sing 0.97 N N



ALX : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
ALX 4ra1 Open in New Window Bound ligand 1 1
ALX 8cb9 Open in New Window Bound ligand 1 1
ALX 8cdo Open in New Window Bound ligand 1 1
ALX 8ch3 Open in New Window Bound ligand 1 1
ALX 8ci6 Open in New Window Bound ligand 1 1
ALX 8cko Open in New Window Bound ligand 1 1
ALX 8cay Open in New Window Sub-component 1 1
ALX 8chc Open in New Window Sub-component 1 1
ALX 8ckd Open in New Window Sub-component 1 1