Chemical Components in the PDB

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04N : Summary

Code

04N

One-letter code

X

Molecule name

2-amino-2-deoxy-4,6-O-(phenylmethylidene)-alpha-D-glucopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranose
OpenEye OEToolkits 1.9.2 (2R,4aR,6S,7R,8R,8aS)-7-azanyl-2-phenyl-4,4a,6,7,8,8a-hexahydropyrano[3,2-d][1,3]dioxine-6,8-diol

Formula

C13 H17 N O5

Formal charge

0

Molecular weight

267.278 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O1C(O)C(N)C(O)C2OC(OCC12)c3ccccc3
SMILES CACTVS 3.385 N[CH]1[CH](O)O[CH]2CO[CH](O[CH]2[CH]1O)c3ccccc3
SMILES OpenEye OEToolkits 1.9.2 c1ccc(cc1)C2OCC3C(O2)C(C(C(O3)O)N)O
Canonical SMILES CACTVS 3.385 N[C@H]1[C@@H](O)O[C@@H]2CO[C@H](O[C@H]2[C@@H]1O)c3ccccc3
Canonical SMILES OpenEye OEToolkits 1.9.2 c1ccc(cc1)[C@@H]2OC[C@@H]3[C@@H](O2)[C@@H]([C@H]([C@H](O3)O)N)O

IUPAC InChI

InChI=1S/C13H17NO5/c14-9-10(15)11-8(18-12(9)16)6-17-13(19-11)7-4-2-1-3-5-7/h1-5,8-13,15-16H,6,14H2/t8-,9-,10-,11-,12+,13-/m1/s1

IUPAC InChI key

BIHZUORUPXZYTO-WXCVZDNMSA-N

Is part of

ON0
04N

wwPDB Information

Atom count

36 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-07-26

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



04N : Atoms of Molecule

Total Number of Atoms: 36
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 -3.595 -0.708 -0.222
2 O1 O O1 N N N 0 -3.541 -0.567 -1.643
3 C2 C C2 R N N 0 -3.362 0.655 0.433
4 N2 N N2 N N N 0 -4.348 1.617 -0.078
5 C3 C C3 R N N 0 -1.948 1.151 0.106
6 O3 O O3 N N N 0 -1.699 2.379 0.792
7 C4 C C4 S N N 0 -0.946 0.092 0.566
8 O4 O O4 N N N 0 0.391 0.472 0.24
9 C5 C C5 R N N 0 -1.266 -1.228 -0.147
10 O5 O O5 N N N 0 -2.588 -1.633 0.202
11 C6 C C6 N N N 0 -0.235 -2.273 0.284
12 O6 O O6 N N N 0 1.072 -1.759 0.001
13 CAL C CAL N Y N 0 5.248 0.803 -0.571
14 CAM C CAM N Y N 0 5.097 -0.405 0.083
15 CAN C CAN N Y N 0 4.141 1.589 -0.836
16 CAO C CAO N Y N 0 3.839 -0.83 0.47
17 CAP C CAP N Y N 0 2.884 1.164 -0.449
18 CBC C CBC N Y N 0 2.733 -0.045 0.204
19 CBP C CBP R N N 0 1.362 -0.508 0.625
20 H1 H H1 N N N 0 -4.576 -1.085 0.067
21 H2 H H2 N N N 0 -3.472 0.562 1.513
22 HN2 H HN2 N N N 0 -5.288 1.315 0.128
23 HN2A H HN2A N N N 0 -4.176 2.541 0.29
24 H3 H H3 N N N 0 -1.854 1.306 -0.969
25 HO3 H HO3 N N N 0 -2.31 3.091 0.559
26 H4 H H4 N N N 0 -1.032 -0.046 1.643
27 H5 H H5 N N N 0 -1.204 -1.083 -1.225
28 H6 H H6 N N N 0 -0.331 -2.464 1.353
29 H6A H H6A N N N 0 -0.395 -3.197 -0.271
30 HAL H HAL N N N 0 6.231 1.137 -0.87
31 HAM H HAM N N N 0 5.961 -1.019 0.289
32 HAN H HAN N N N 0 4.259 2.533 -1.347
33 HAO H HAO N N N 0 3.722 -1.774 0.98
34 HAP H HAP N N N 0 2.02 1.777 -0.657
35 HBP H HBP N N N 0 1.341 -0.63 1.708
36 H7 H H7 N N Y 0 -3.68 -1.393 -2.126



04N : Chemical Bonds

Total Number of Bonds: 38
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 C2 N2 C N sing 1.47 N N
5 C2 C3 C C sing 1.53 N N
6 C3 O3 C O sing 1.43 N N
7 C3 C4 C C sing 1.53 N N
8 C4 O4 C O sing 1.43 N N
9 C4 C5 C C sing 1.53 N N
10 O4 CBP O C sing 1.43 N N
11 C5 O5 C O sing 1.43 N N
12 C5 C6 C C sing 1.53 N N
13 C6 O6 C O sing 1.43 N N
14 O6 CBP O C sing 1.43 N N
15 CAL CAM C C doub 1.38 N Y
16 CAL CAN C C sing 1.38 N Y
17 CAM CAO C C sing 1.38 N Y
18 CAN CAP C C doub 1.38 N Y
19 CAO CBC C C doub 1.38 N Y
20 CAP CBC C C sing 1.38 N Y
21 CBC CBP C C sing 1.51 N N
22 C1 H1 C H sing 1.09 N N
23 C2 H2 C H sing 1.09 N N
24 N2 HN2 N H sing 1.01 N N
25 N2 HN2A N H sing 1.01 N N
26 C3 H3 C H sing 1.09 N N
27 O3 HO3 O H sing 0.97 N N
28 C4 H4 C H sing 1.09 N N
29 C5 H5 C H sing 1.09 N N
30 C6 H6 C H sing 1.09 N N
31 C6 H6A C H sing 1.09 N N
32 CAL HAL C H sing 1.08 N N
33 CAM HAM C H sing 1.08 N N
34 CAN HAN C H sing 1.08 N N
35 CAO HAO C H sing 1.08 N N
36 CAP HAP C H sing 1.08 N N
37 CBP HBP C H sing 1.09 N N
38 O1 H7 O H sing 0.97 N N



04N : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct
04N 4b3m Open in New Window Sub-component 1 1