Chemical Components in the PDB

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AXP : Summary

Code

AXP

One-letter code

X

Molecule name

(1S)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol

Systematic names

ProgramVersionName
ACDLabs 10.04 (1S)-4-(acetylamino)-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol
OpenEye OEToolkits 1.5.0 [(2S,4S,5R,6R)-5-acetamido-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxan-2-yl]phosphonic acid

Formula

C10 H20 N O9 P

Formal charge

0

Molecular weight

329.241 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)C1OC(C(NC(=O)C)C(O)C1)C(O)C(O)CO
SMILES CACTVS 3.341 CC(=O)N[CH]1[CH](O)C[CH](O[CH]1[CH](O)[CH](O)CO)[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC1C(CC(OC1C(C(CO)O)O)P(=O)(O)O)O
Canonical SMILES CACTVS 3.341 CC(=O)N[C@@H]1[C@@H](O)C[C@@H](O[C@H]1[C@H](O)[C@H](O)CO)[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)N[C@@H]1[C@H](C[C@@H](O[C@H]1[C@@H]([C@@H](CO)O)O)P(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H20NO9P/c1-4(13)11-8-5(14)2-7(21(17,18)19)20-10(8)9(16)6(15)3-12/h5-10,12,14-16H,2-3H2,1H3,(H,11,13)(H2,17,18,19)/t5-,6+,7-,8+,9+,10+/m0/s1

IUPAC InChI key

QITAGYVZDNZULE-HDBWYCHPSA-N
AXP

wwPDB Information

Atom count

41 (21 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



AXP : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P1 P P1 N N N 0 -0.701 -0.087 -3.197
2 C2 C C2 S N N 0 -0.428 -0.223 -1.4
3 C3 C C3 N N N 0 0.679 -1.243 -1.128
4 C4 C C4 S N N 0 0.878 -1.373 0.385
5 C5 C C5 R N N 0 1.12 0.022 0.97
6 C6 C C6 R N N 0 -0.02 0.948 0.542
7 C7 C C7 R N N 0 -1.35 0.377 1.037
8 C8 C C8 R N N 0 -1.394 0.439 2.565
9 C9 C C9 N N N 0 -2.783 0.022 3.053
10 C10 C C10 N N N 0 3.531 0.318 1.153
11 C11 C C11 N N N 0 4.84 0.86 0.64
12 N5 N N5 N N N 0 2.392 0.549 0.471
13 O1P O O1P N N N 0 -1.101 -1.406 -3.736
14 O2P O O2P N N N 0 0.659 0.393 -3.912
15 O3P O O3P N N N 0 -1.866 0.985 -3.484
16 O4 O O4 N N N 0 -0.288 -1.946 0.978
17 O6 O O6 N N N 0 -0.049 1.05 -0.882
18 O7 O O7 N N N 0 -2.429 1.144 0.498
19 O8 O O8 N N N 0 -0.414 -0.447 3.107
20 O9 O O9 N N N 0 -2.825 0.081 4.48
21 O10 O O10 N N N 0 3.503 -0.325 2.18
22 H2 H H2 N N N 0 -1.349 -0.551 -0.917
23 H32 H H31 N N N 0 1.607 -0.906 -1.591
24 H31 H H32 N N N 0 0.394 -2.21 -1.543
25 H4 H H4 N N N 0 1.741 -2.008 0.587
26 H5 H H5 N N N 0 1.151 -0.038 2.057
27 H6 H H6 N N N 0 0.131 1.937 0.973
28 H7 H H7 N N N 0 -1.444 -0.659 0.713
29 H8 H H8 N N N 0 -1.185 1.457 2.894
30 H92 H H91 N N N 0 -3.532 0.699 2.64
31 H91 H H92 N N N 0 -2.993 -0.995 2.725
32 H111 H H111 N N N 0 5.643 0.574 1.319
33 H113 H H112 N N N 0 5.039 0.452 -0.35
34 H112 H H113 N N N 0 4.785 1.947 0.58
35 HN5 H HN5 N N N 0 2.415 1.065 -0.35
36 HOP2 H HOP2 N N N 0 0.884 1.253 -3.533
37 HOP3 H HOP3 N N N 0 -1.978 1.026 -4.443
38 HO4 H HO4 N N Y 0 -0.401 -2.821 0.582
39 HO7 H HO7 N N Y 0 -2.266 2.065 0.742
40 HO8 H HO8 N N Y 0 -0.715 -1.346 2.918
41 HO9 H HO9 N N Y 0 -3.715 -0.188 4.745



AXP : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P1 C2 P C sing 1.82 N N
2 P1 O1P P O doub 1.48 N N
3 P1 O2P P O sing 1.61 N N
4 P1 O3P P O sing 1.61 N N
5 C2 C3 C C sing 1.53 N N
6 C2 O6 C O sing 1.43 N N
7 C2 H2 C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 H32 C H sing 1.09 N N
10 C3 H31 C H sing 1.09 N N
11 C4 C5 C C sing 1.53 N N
12 C4 O4 C O sing 1.43 N N
13 C4 H4 C H sing 1.09 N N
14 C5 C6 C C sing 1.53 N N
15 C5 N5 C N sing 1.46 N N
16 C5 H5 C H sing 1.09 N N
17 C6 C7 C C sing 1.53 N N
18 C6 O6 C O sing 1.43 N N
19 C6 H6 C H sing 1.09 N N
20 C7 C8 C C sing 1.53 N N
21 C7 O7 C O sing 1.43 N N
22 C7 H7 C H sing 1.09 N N
23 C8 C9 C C sing 1.53 N N
24 C8 O8 C O sing 1.43 N N
25 C8 H8 C H sing 1.09 N N
26 C9 O9 C O sing 1.43 N N
27 C9 H92 C H sing 1.09 N N
28 C9 H91 C H sing 1.09 N N
29 C10 C11 C C sing 1.51 N N
30 C10 N5 C N sing 1.35 N N
31 C10 O10 C O doub 1.21 N N
32 C11 H111 C H sing 1.09 N N
33 C11 H113 C H sing 1.09 N N
34 C11 H112 C H sing 1.09 N N
35 N5 HN5 N H sing 0.97 N N
36 O2P HOP2 O H sing 0.97 N N
37 O3P HOP3 O H sing 0.97 N N
38 O4 HO4 O H sing 0.97 N N
39 O7 HO7 O H sing 0.97 N N
40 O8 HO8 O H sing 0.97 N N
41 O9 HO9 O H sing 0.97 N N



AXP : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
AXP 1dil Open in New Window Bound ligand 1 1
AXP 1inw Open in New Window Bound ligand 1 1