Chemical Components in the PDB

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M3N : Summary

Code

M3N

One-letter code

X

Molecule name

4-(hydroxymethyl)-1-(alpha-D-mannopyranosyl)-1H-1,2,3-triazole

Systematic names

ProgramVersionName
ACDLabs 12.01 4-(hydroxymethyl)-1-(alpha-D-mannopyranosyl)-1H-1,2,3-triazole
OpenEye OEToolkits 1.9.2 (2R,3S,4S,5S,6S)-2-(hydroxymethyl)-6-[4-(hydroxymethyl)-1,2,3-triazol-1-yl]oxane-3,4,5-triol

Formula

C9 H15 N3 O6

Formal charge

0

Molecular weight

261.232 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n1nn(cc1CO)C2OC(C(O)C(O)C2O)CO
SMILES CACTVS 3.385 OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)n2cc(CO)nn2
SMILES OpenEye OEToolkits 1.9.2 c1c(nnn1C2C(C(C(C(O2)CO)O)O)O)CO
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@@H]([C@@H](O)[C@@H](O)[C@@H]1O)n2cc(CO)nn2
Canonical SMILES OpenEye OEToolkits 1.9.2 c1c(nnn1[C@@H]2[C@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)CO

IUPAC InChI

InChI=1S/C9H15N3O6/c13-2-4-1-12(11-10-4)9-8(17)7(16)6(15)5(3-14)18-9/h1,5-9,13-17H,2-3H2/t5-,6-,7+,8+,9+/m1/s1

IUPAC InChI key

BHGZOVXPACYZLI-DFTQBPQZSA-N
M3N

wwPDB Information

Atom count

33 (18 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2014-05-02

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



M3N : Atoms of Molecule

Total Number of Atoms: 33
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 -0.079 0.398 -1.269
2 C2 C C2 S N N 0 -0.928 1.603 -0.854
3 O2 O O2 N N N 0 -1.977 1.798 -1.804
4 C3 C C3 S N N 0 -1.531 1.34 0.529
5 O3 O O3 N N N 0 -2.383 2.428 0.893
6 C4 C C4 S N N 0 -2.347 0.044 0.481
7 O4 O O4 N N N 0 -2.856 -0.248 1.783
8 C5 C C5 R N N 0 -1.444 -1.1 0.014
9 O5 O O5 N N N 0 -0.891 -0.779 -1.264
10 C6 C C6 N N N 0 -2.266 -2.386 -0.095
11 O6 O O6 N N N 0 -1.402 -3.478 -0.417
12 C01 C C01 N Y N 0 3.008 0.02 0.522
13 C02 C C02 N Y N 0 2.342 0.18 -0.645
14 N03 N N03 N Y N 0 1.028 0.231 -0.325
15 N04 N N04 N Y N 0 0.919 0.108 0.952
16 N05 N N05 N Y N 0 2.082 -0.02 1.486
17 C03 C C03 N N N 0 4.5 -0.098 0.7
18 O01 O O01 N N N 0 5.14 -0.008 -0.575
19 H1 H H1 N N N 0 0.318 0.561 -2.271
20 H2 H H2 N N N 0 -0.301 2.493 -0.816
21 HO2 H H3 N N Y 0 -2.555 2.547 -1.603
22 H3 H H4 N N N 0 -0.732 1.242 1.263
23 HO3 H H5 N N Y 0 -1.933 3.283 0.936
24 H4 H H6 N N N 0 -3.176 0.162 -0.217
25 HO4 H H7 N N Y 0 -3.434 0.439 2.143
26 H5 H H8 N N N 0 -0.638 -1.244 0.733
27 H61 H H9 N N N 0 -2.76 -2.583 0.856
28 H62 H H10 N N N 0 -3.016 -2.273 -0.878
29 HO6 H H11 N N Y 0 -1.856 -4.327 -0.502
30 H12 H H12 N N N 0 2.772 0.254 -1.633
31 H13 H H13 N N N 0 4.855 0.708 1.342
32 H14 H H14 N N N 0 4.737 -1.059 1.158
33 H15 H H15 N N N 0 6.104 -0.076 -0.537



M3N : Chemical Bonds

Total Number of Bonds: 34
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 O4 C4 O C sing 1.43 N N
4 C5 C4 C C sing 1.53 N N
5 C5 O5 C O sing 1.43 N N
6 C4 C3 C C sing 1.53 N N
7 O5 C1 O C sing 1.43 N N
8 O01 C03 O C sing 1.43 N N
9 C3 O3 C O sing 1.43 N N
10 C3 C2 C C sing 1.53 N N
11 C02 N03 C N sing 1.35 N Y
12 C02 C01 C C doub 1.35 N Y
13 C03 C01 C C sing 1.51 N N
14 C1 C2 C C sing 1.53 N N
15 C1 N03 C N sing 1.46 N N
16 C2 O2 C O sing 1.43 N N
17 N03 N04 N N sing 1.29 N Y
18 C01 N05 C N sing 1.34 N Y
19 N04 N05 N N doub 1.29 N Y
20 C1 H1 C H sing 1.09 N N
21 C2 H2 C H sing 1.09 N N
22 O2 HO2 O H sing 0.97 N N
23 C3 H3 C H sing 1.09 N N
24 O3 HO3 O H sing 0.97 N N
25 C4 H4 C H sing 1.09 N N
26 O4 HO4 O H sing 0.97 N N
27 C5 H5 C H sing 1.09 N N
28 C6 H61 C H sing 1.09 N N
29 C6 H62 C H sing 1.09 N N
30 O6 HO6 O H sing 0.97 N N
31 C02 H12 C H sing 1.08 N N
32 C03 H13 C H sing 1.09 N N
33 C03 H14 C H sing 1.09 N N
34 O01 H15 O H sing 0.97 N N



M3N : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
M3N 4pf5 Open in New Window Bound ligand 2 1