Chemical Components in the PDB

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RST : Summary

Code

RST

One-letter code

X

Molecule name

3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose
OpenEye OEToolkits 1.7.6 (2R,4R,5R,6S)-4-azanyl-6-methyl-oxane-2,5-diol

Formula

C6 H13 N O3

Formal charge

0

Molecular weight

147.172 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC1C(OC(O)CC1N)C
SMILES CACTVS 3.370 C[CH]1O[CH](O)C[CH](N)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 CC1C(C(CC(O1)O)N)O
Canonical SMILES CACTVS 3.370 C[C@@H]1O[C@@H](O)C[C@@H](N)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H]1[C@@H]([C@@H](C[C@@H](O1)O)N)O

IUPAC InChI

InChI=1S/C6H13NO3/c1-3-6(9)4(7)2-5(8)10-3/h3-6,8-9H,2,7H2,1H3/t3-,4+,5+,6-/m0/s1

IUPAC InChI key

BBMKQGIZNKEDOX-KCDKBNATSA-N
RST

wwPDB Information

Atom count

23 (10 without Hydrogen)

Polymer type

Saccharide

Type description

L-saccharide, alpha linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2002-09-02

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



RST : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -1.41 0.495 -0.215
2 O1 O O1 N N Y 0 -2.514 1.242 0.299
3 C2 C C2 N N N 0 -0.152 1.368 -0.2
4 C3 C C3 R N N 0 1.039 0.542 -0.695
5 N3 N N3 N N N 0 2.265 1.348 -0.612
6 C4 C C4 R N N 0 1.185 -0.703 0.185
7 O4 O O4 N N N 0 1.472 -0.308 1.528
8 C5 C C5 S N N 0 -0.125 -1.496 0.155
9 O5 O O5 N N N 0 -1.196 -0.66 0.598
10 C6 C C6 N N N 0 -0.403 -1.967 -1.274
11 HN31 H HN31 N N N 0 2.19 2.179 -1.18
12 H1 H H1 N N N 0 -1.625 0.186 -1.238
13 HO1 H HO1 N N Y 0 -3.346 0.75 0.318
14 H2 H H21 N N N 0 -0.297 2.227 -0.854
15 H22 H H22 N N N 0 0.041 1.711 0.817
16 H3 H H3 N N N 0 0.87 0.241 -1.729
17 HN32 H HN32 N N N 0 2.48 1.582 0.345
18 H4 H H4 N N N 0 1.996 -1.324 -0.194
19 HO4 H HO4 N N Y 0 1.577 -1.048 2.142
20 H5 H H5 N N N 0 -0.042 -2.361 0.813
21 H61 H H61 N N N 0 0.415 -2.604 -1.612
22 H62 H H62 N N N 0 -1.335 -2.532 -1.296
23 H63 H H63 N N N 0 -0.486 -1.102 -1.932



RST : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O sing 1.43 N N
2 C1 C2 C C sing 1.53 N N
3 C1 O5 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 O1 HO1 O H sing 0.97 N N
6 C2 C3 C C sing 1.53 N N
7 C2 H2 C H sing 1.09 N N
8 C2 H22 C H sing 1.09 N N
9 C3 N3 C N sing 1.47 N N
10 C3 C4 C C sing 1.53 N N
11 C3 H3 C H sing 1.09 N N
12 N3 HN31 N H sing 1.01 N N
13 N3 HN32 N H sing 1.01 N N
14 C4 O4 C O sing 1.43 N N
15 C4 C5 C C sing 1.53 N N
16 C4 H4 C H sing 1.09 N N
17 O4 HO4 O H sing 0.97 N N
18 C5 O5 C O sing 1.43 N N
19 C5 C6 C C sing 1.53 N N
20 C5 H5 C H sing 1.09 N N
21 C6 H61 C H sing 1.09 N N
22 C6 H62 C H sing 1.09 N N
23 C6 H63 C H sing 1.09 N N



RST : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
RST 3rum Open in New Window Bound ligand 2 1