Chemical Components in the PDB

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CBF : Summary

Code

CBF

One-letter code

X

Molecule name

(2R,3R,4S,5S,6R)-2,3,4,5-tetrahydroxy-6-(hydroxymethyl)oxane-2-carboxamide

Systematic names

ProgramVersionName
ACDLabs 11.02 (2R,3R,4S,5S,6R)-2,3,4,5-tetrahydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-carboxamide (non-preferred name)
OpenEye OEToolkits 1.6.1 (2R,3R,4S,5S,6R)-2,3,4,5-tetrahydroxy-6-(hydroxymethyl)oxane-2-carboxamide

Formula

C7 H13 N O7

Formal charge

0

Molecular weight

223.181 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=C(N)C1(O)OC(C(O)C(O)C1O)CO
SMILES CACTVS 3.352 NC(=O)[C]1(O)O[CH](CO)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.0 C(C1C(C(C(C(O1)(C(=O)N)O)O)O)O)O
Canonical SMILES CACTVS 3.352 NC(=O)[C@]1(O)O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.0 C([C@@H]1[C@H]([C@@H]([C@H]([C@@](O1)(C(=O)N)O)O)O)O)O

IUPAC InChI

InChI=1S/C7H13NO7/c8-6(13)7(14)5(12)4(11)3(10)2(1-9)15-7/h2-5,9-12,14H,1H2,(H2,8,13)/t2-,3-,4+,5-,7-/m1/s1

IUPAC InChI key

DTZYCNDAJQDPQC-UHKLXPPTSA-N
CBF

wwPDB Information

Atom count

28 (15 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, alpha linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2003-05-01

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



CBF : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O6 O O6 N N N 0 2.364 2.855 0.148
2 C6 C C6 N N N 0 2.506 1.548 -0.41
3 C5 C C5 R N N 0 1.424 0.629 0.161
4 O5 O O5 N N N 0 0.139 1.084 -0.266
5 C1 C C1 R N N 0 -0.951 0.308 0.235
6 O1 O O1 N N N 0 -0.929 0.321 1.664
7 C7 C C7 N N N 0 -2.252 0.893 -0.253
8 O7 O O7 N N N 0 -3.039 1.366 0.539
9 N1 N N1 N N N 0 -2.54 0.89 -1.57
10 C2 C C2 R N N 0 -0.821 -1.134 -0.264
11 O2 O O2 N N N 0 -1.877 -1.926 0.282
12 C3 C C3 S N N 0 0.529 -1.701 0.185
13 O3 O O3 N N N 0 0.691 -3.021 -0.338
14 C4 C C4 S N N 0 1.65 -0.799 -0.342
15 O4 O O4 N N N 0 2.91 -1.278 0.132
16 HO6 H HO6 N N N 0 3.019 3.492 -0.17
17 H61 H H61 N N N 0 2.402 1.602 -1.494
18 H62 H H62 N N N 0 3.49 1.15 -0.159
19 H5 H H5 N N N 0 1.472 0.644 1.249
20 HO1 H HO1 N N N 0 -1.007 1.204 2.05
21 HN11 H HN11 N N N 0 -1.91 0.512 -2.203
22 HN12 H HN12 N N N 0 -3.377 1.267 -1.884
23 H2 H H2 N N N 0 -0.879 -1.149 -1.352
24 HO2 H HO2 N N N 0 -2.763 -1.62 0.042
25 H3 H H3 N N N 0 0.567 -1.733 1.274
26 HO3 H HO3 N N N 0 0.01 -3.644 -0.051
27 H4 H H4 N N N 0 1.643 -0.808 -1.431
28 HO4 H HO4 N N N 0 3.667 -0.751 -0.16



CBF : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C sing 1.43 N N
2 O6 HO6 O H sing 0.97 N N
3 C6 C5 C C sing 1.53 N N
4 C6 H61 C H sing 1.09 N N
5 C6 H62 C H sing 1.09 N N
6 C5 O5 C O sing 1.43 N N
7 C5 C4 C C sing 1.53 N N
8 C5 H5 C H sing 1.09 N N
9 O5 C1 O C sing 1.43 N N
10 C1 O1 C O sing 1.43 N N
11 C1 C7 C C sing 1.51 N N
12 C1 C2 C C sing 1.53 N N
13 O1 HO1 O H sing 0.97 N N
14 C7 O7 C O doub 1.21 N N
15 C7 N1 C N sing 1.35 N N
16 N1 HN11 N H sing 0.97 N N
17 N1 HN12 N H sing 0.97 N N
18 C2 O2 C O sing 1.43 N N
19 C2 C3 C C sing 1.53 N N
20 C2 H2 C H sing 1.09 N N
21 O2 HO2 O H sing 0.97 N N
22 C3 O3 C O sing 1.43 N N
23 C3 C4 C C sing 1.53 N N
24 C3 H3 C H sing 1.09 N N
25 O3 HO3 O H sing 0.97 N N
26 C4 O4 C O sing 1.43 N N
27 C4 H4 C H sing 1.09 N N
28 O4 HO4 O H sing 0.97 N N



CBF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
CBF 1p4j Open in New Window Bound ligand 1 1