Chemical Components in the PDB

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RNS : Summary

Code

RNS

One-letter code

X

Molecule name

L-RHAMNOSE

Systematic names

ProgramVersionName
ACDLabs 10.04 6-deoxy-L-mannose
OpenEye OEToolkits 1.5.0 (2R,3R,4S,5S)-2,3,4,5-tetrahydroxyhexanal

Formula

C6 H12 O5

Formal charge

0

Molecular weight

164.156 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=CC(O)C(O)C(O)C(O)C
SMILES CACTVS 3.341 C[CH](O)[CH](O)[CH](O)[CH](O)C=O
SMILES OpenEye OEToolkits 1.5.0 CC(C(C(C(C=O)O)O)O)O
Canonical SMILES CACTVS 3.341 C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@@H]([C@@H]([C@H]([C@H](C=O)O)O)O)O

IUPAC InChI

InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h2-6,8-11H,1H3/t3-,4-,5-,6-/m0/s1

IUPAC InChI key

PNNNRSAQSRJVSB-BXKVDMCESA-N
RNS

wwPDB Information

Atom count

23 (11 without Hydrogen)

Polymer type

Saccharide

Type description

L-SACCHARIDE

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

1999-11-19

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



RNS : 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 N N N 0 0.32 0.41 -2.749
2 C2 C C2 R N N 0 -0.495 0.064 -1.53
3 C3 C C3 R N N 0 0.368 0.221 -0.277
4 C4 C C4 S N N 0 -0.46 -0.13 0.959
5 C5 C C5 S N N 0 0.403 0.026 2.212
6 C6 C C6 N N N 0 -0.424 -0.325 3.45
7 O1 O O1 N N N 0 0.494 -0.414 -3.614
8 O2 O O2 N N N 0 -1.621 0.941 -1.446
9 O3 O O3 N N N 0 1.493 -0.655 -0.362
10 O4 O O4 N N N 0 -0.915 -1.481 0.86
11 O5 O O5 N N N 0 0.858 1.377 2.312
12 H11 H H11 N N N 0 0.749 1.396 -2.85
13 H2 H H2 N N N 0 -0.842 -0.966 -1.606
14 H3 H H3 N N N 0 0.715 1.251 -0.202
15 H4 H H4 N N N 0 -1.318 0.538 1.024
16 H5 H H5 N N N 0 1.262 -0.642 2.148
17 H61 H 1H6 N N N 0 0.19 -0.213 4.343
18 H62 H 2H6 N N N 0 -1.283 0.343 3.514
19 H63 H 3H6 N N N 0 -0.771 -1.355 3.374
20 HO2 H HO2 N N N 0 -1.27 1.839 -1.381
21 HO3 H HO3 N N N 0 1.143 -1.554 -0.427
22 HO4 H HO4 N N N 0 -0.126 -2.038 0.805
23 HO5 H HO5 N N N 0 0.07 1.934 2.366



RNS : Chemical Bonds

Total Number of Bonds: 22
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.51 N N
2 C1 O1 C O doub 1.21 N N
3 C1 H11 C H sing 1.08 N N
4 C2 C3 C C sing 1.53 N N
5 C2 O2 C O sing 1.43 N N
6 C2 H2 C H sing 1.09 N N
7 C3 C4 C C sing 1.53 N N
8 C3 O3 C O sing 1.43 N N
9 C3 H3 C H sing 1.09 N N
10 C4 C5 C C sing 1.53 N N
11 C4 O4 C O sing 1.43 N N
12 C4 H4 C H sing 1.09 N N
13 C5 C6 C C sing 1.53 N N
14 C5 O5 C O sing 1.43 N N
15 C5 H5 C H sing 1.09 N N
16 C6 H61 C H sing 1.09 N N
17 C6 H62 C H sing 1.09 N N
18 C6 H63 C H sing 1.09 N N
19 O2 HO2 O H sing 0.97 N N
20 O3 HO3 O H sing 0.97 N N
21 O4 HO4 O H sing 0.97 N N
22 O5 HO5 O H sing 0.97 N N



RNS : Used in PDB Entries

Total Number of PDB Entries: 8
Ligand Code PDB Entry ID Type Total Distinct
RNS 1de6 Open in New Window Bound ligand 4 1
RNS 1x8d Open in New Window Bound ligand 4 1
RNS 2i56 Open in New Window Bound ligand 4 1
RNS 3itt Open in New Window Bound ligand 4 1
RNS 3m0h Open in New Window Bound ligand 4 1
RNS 3m0v Open in New Window Bound ligand 4 1
RNS 3m0y Open in New Window Bound ligand 4 1
RNS 4gji Open in New Window Bound ligand 4 1