Chemical Components in the PDB

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5KV : Summary

Code

5KV

One-letter code

X

Molecule name

2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose
OpenEye OEToolkits 1.9.2 [(2R,3R,4R,5S,6R)-2,4,5-tris(oxidanyl)-6-(sulfooxymethyl)oxan-3-yl]sulfamic acid

Formula

C6 H13 N O11 S2

Formal charge

0

Molecular weight

339.298 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC1C(C(C(OC1COS(=O)(O)=O)O)NS(O)(=O)=O)O
SMILES CACTVS 3.385 O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O)[CH](O)[CH]1N[S](O)(=O)=O
SMILES OpenEye OEToolkits 1.9.2 C(C1C(C(C(C(O1)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O
Canonical SMILES CACTVS 3.385 O[C@@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1N[S](O)(=O)=O
Canonical SMILES OpenEye OEToolkits 1.9.2 C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O

IUPAC InChI

InChI=1S/C6H13NO11S2/c8-4-2(1-17-20(14,15)16)18-6(10)3(5(4)9)7-19(11,12)13/h2-10H,1H2,(H,11,12,13)(H,14,15,16)/t2-,3-,4-,5-,6-/m1/s1

IUPAC InChI key

DQTRACMFIGDHSN-QZABAPFNSA-N
5KV

wwPDB Information

Atom count

33 (20 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, beta linking

Type code

ATOMS

Is modified

Yes

Standard parent

GCS

Defined at

2015-10-15

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



5KV : 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 O4 O O13 N N N 0 0.834 2.969 -0.176
2 C3 C C18 R N N 0 -1.195 1.668 -0.387
3 C4 C C19 S N N 0 0.231 1.721 0.171
4 C5 C C20 R N N 0 1.048 0.573 -0.429
5 C2 C C21 R N N 0 -1.803 0.298 -0.076
6 C1 C C22 R N N 0 -0.908 -0.795 -0.666
7 O5 O O25 N N N 0 0.411 -0.67 -0.13
8 O1 O O28 N N Y 0 -1.439 -2.079 -0.332
9 N2 N N29 N N N 0 -3.14 0.209 -0.669
10 O3 O O30 N N N 0 -1.985 2.691 0.223
11 C6 C C31 N N N 0 2.456 0.582 0.169
12 O6 O O32 N N N 0 3.253 -0.414 -0.475
13 S33 S S33 N N N 0 4.682 -0.494 0.043
14 S34 S S34 N N N 0 -4.337 -0.63 0.109
15 O35 O O35 N N N 0 -3.778 -1.885 0.471
16 O36 O O36 N N N 0 -4.627 0.103 1.411
17 O37 O O37 N N N 0 -5.503 -0.501 -0.692
18 O38 O O38 N N N 0 5.096 0.843 0.287
19 O39 O O39 N N N 0 4.63 -1.182 1.4
20 O40 O O40 N N N 0 5.376 -1.377 -0.828
21 HO4 H H1 N N Y 0 1.74 3.07 0.146
22 H3 H H2 N N N 0 -1.17 1.82 -1.466
23 H4 H H3 N N N 0 0.202 1.62 1.256
24 H5 H H4 N N N 0 1.11 0.698 -1.51
25 H2 H H5 N N N 0 -1.873 0.167 1.004
26 H1 H H6 N N N 0 -0.871 -0.688 -1.75
27 HO1 H H7 N N Y 0 -0.921 -2.82 -0.675
28 HN21 H H8 N N N 0 -3.323 0.642 -1.518
29 HO3 H H9 N N Y 0 -1.653 3.587 0.073
30 H61 H H10 N N N 0 2.908 1.562 0.018
31 H62 H H11 N N N 0 2.399 0.368 1.236
32 H12 H H12 N N N 0 -5.319 -0.308 1.948
33 H13 H H13 N N N 0 5.495 -1.285 1.822



5KV : Chemical Bonds

Total Number of Bonds: 33
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C3 O C sing 1.43 N N
2 O4 C4 O C sing 1.43 N N
3 C3 C4 C C sing 1.53 N N
4 C3 C2 C C sing 1.53 N N
5 O37 S34 O S doub 1.42 N N
6 C4 C5 C C sing 1.53 N N
7 O35 S34 O S doub 1.42 N N
8 N2 S34 N S sing 1.66 N N
9 N2 C2 N C sing 1.47 N N
10 S34 O36 S O sing 1.52 N N
11 C2 C1 C C sing 1.53 N N
12 C5 C6 C C sing 1.53 N N
13 C5 O5 C O sing 1.43 N N
14 C1 O5 C O sing 1.43 N N
15 C1 O1 C O sing 1.43 N N
16 C6 O6 C O sing 1.43 N N
17 O6 S33 O S sing 1.52 N N
18 O38 S33 O S doub 1.42 N N
19 S33 O40 S O doub 1.42 N N
20 S33 O39 S O sing 1.52 N N
21 O4 HO4 O H sing 0.97 N N
22 C3 H3 C H sing 1.09 N N
23 C4 H4 C H sing 1.09 N N
24 C5 H5 C H sing 1.09 N N
25 C2 H2 C H sing 1.09 N N
26 C1 H1 C H sing 1.09 N N
27 O1 HO1 O H sing 0.97 N N
28 N2 HN21 N H sing 0.97 N N
29 O3 HO3 O H sing 0.97 N N
30 C6 H61 C H sing 1.09 N N
31 C6 H62 C H sing 1.09 N N
32 O36 H12 O H sing 0.97 N N
33 O39 H13 O H sing 0.97 N N



5KV : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5KV 5e9c Open in New Window s 1 1