Chemical Components in the PDB

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MFB : Summary

Code

MFB

One-letter code

X

Molecule name

methyl beta-L-fucopyranoside

Synonyms

BETA-L-METHYL-FUCOSE
methyl 6-deoxy-beta-L-galactopyranoside
methyl beta-L-fucoside
methyl L-fucoside
methyl fucoside

Systematic names

ProgramVersionName
ACDLabs 10.04 methyl 6-deoxy-beta-L-galactopyranoside
OpenEye OEToolkits 1.5.0 (2S,3S,4R,5S,6S)-2-methoxy-6-methyl-oxane-3,4,5-triol

Formula

C7 H14 O5

Formal charge

0

Molecular weight

178.183 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(O)C(O)C(OC1OC)C
SMILES CACTVS 3.341 CO[CH]1O[CH](C)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 CC1C(C(C(C(O1)OC)O)O)O
Canonical SMILES CACTVS 3.341 CO[C@H]1O[C@@H](C)[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)OC)O)O)O

IUPAC InChI

InChI=1S/C7H14O5/c1-3-4(8)5(9)6(10)7(11-2)12-3/h3-10H,1-2H3/t3-,4+,5+,6-,7-/m0/s1

IUPAC InChI key

OHWCAVRRXKJCRB-XUVCUMPTSA-N
MFB

wwPDB Information

Atom count

26 (12 without Hydrogen)

Polymer type

Saccharide

Type description

L-saccharide

Type code

ATOMS

Is modified

Yes

Standard parent

FUL

Defined at

1999-07-08

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



MFB : Atoms of Molecule

Total Number of Atoms: 26
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 1.688 -2.499 2.445
2 C2 C C2 S N N 0 0.54 -3.041 1.59
3 C3 C C3 R N N 0 -0.294 -1.894 1.016
4 C4 C C4 S N N 0 0.597 -0.857 0.333
5 C5 C C5 S N N 0 1.705 -0.411 1.292
6 C6 C C6 N N N 0 2.677 0.567 0.642
7 CM C CM N N N 0 3.596 -3.103 3.677
8 H1 H H1 N N N 0 1.305 -2.025 3.357
9 H2 H H2 N N N 0 0.915 -3.676 0.778
10 H3 H H3 N N N 0 -0.869 -1.415 1.818
11 H4 H H4 N N N 0 -0.0010 0.0 0.0010
12 H5 H H5 N N N 0 1.268 0.071 2.176
13 H61 H H61 N N N 0 2.999 1.326 1.361
14 H62 H H62 N N N 0 3.564 0.042 0.275
15 H63 H H63 N N N 0 2.203 1.074 -0.204
16 HM1 H HM1 N N N 0 3.258 -2.976 4.709
17 HM2 H HM2 N N N 0 3.955 -2.15 3.28
18 HM3 H HM3 N N N 0 4.406 -3.836 3.649
19 HO2 H HO2 N N Y 0 -1.216 -3.675 2.111
20 HO3 H HO3 N N Y 0 -0.737 -2.624 -0.725
21 HO4 H HO4 N N Y 0 1.763 -2.148 -0.522
22 O1 O O1 N N N 0 2.52 -3.574 2.881
23 O2 O O2 N N N 0 -0.308 -3.854 2.399
24 O3 O O3 N N N 0 -1.238 -2.396 0.074
25 O4 O O4 N N N 0 1.194 -1.429 -0.833
26 O5 O O5 N N N 0 2.465 -1.548 1.719



MFB : Chemical Bonds

Total Number of Bonds: 26
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 C1 H1 C H sing 1.1 N N
5 C2 C3 C C sing 1.53 N N
6 C2 O2 C O sing 1.43 N N
7 C2 H2 C H sing 1.1 N N
8 C3 C4 C C sing 1.53 N N
9 C3 O3 C O sing 1.42 N N
10 C3 H3 C H sing 1.1 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 1.1 N N
14 C5 C6 C C sing 1.52 N N
15 C5 O5 C O sing 1.43 N N
16 C5 H5 C H sing 1.1 N N
17 C6 H61 C H sing 1.09 N N
18 C6 H62 C H sing 1.09 N N
19 C6 H63 C H sing 1.09 N N
20 O1 CM O C sing 1.42 N N
21 O2 HO2 O H sing 0.97 N N
22 O3 HO3 O H sing 0.97 N N
23 O4 HO4 O H sing 0.97 N N
24 CM HM1 C H sing 1.09 N N
25 CM HM2 C H sing 1.09 N N
26 CM HM3 C H sing 1.09 N N



MFB : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
MFB 1kwx Open in New Window Bound ligand 3 1
MFB 1rdj Open in New Window Bound ligand 2 1
MFB 4c1y Open in New Window Bound ligand 12 1