Chemical Components in the PDB

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16Z : Summary

Code

16Z

One-letter code

X

Molecule name

(2S,3S,4R,5S)-2-(4-methoxyphenyl)-1,5-dimethylpyrrolidine-3,4-diol

Synonyms

4-epi-(+)-Codonopsinine

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S,3S,4R,5S)-2-(4-methoxyphenyl)-1,5-dimethylpyrrolidine-3,4-diol
OpenEye OEToolkits 1.7.6 (2S,3S,4R,5S)-2-(4-methoxyphenyl)-1,5-dimethyl-pyrrolidine-3,4-diol

Formula

C13 H19 N O3

Formal charge

0

Molecular weight

237.295 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC2C(c1ccc(OC)cc1)N(C)C(C)C2O
SMILES CACTVS 3.370 COc1ccc(cc1)[CH]2[CH](O)[CH](O)[CH](C)N2C
SMILES OpenEye OEToolkits 1.7.6 CC1C(C(C(N1C)c2ccc(cc2)OC)O)O
Canonical SMILES CACTVS 3.370 COc1ccc(cc1)[C@H]2[C@H](O)[C@H](O)[C@H](C)N2C
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H]1[C@H]([C@H]([C@@H](N1C)c2ccc(cc2)OC)O)O

IUPAC InChI

InChI=1S/C13H19NO3/c1-8-12(15)13(16)11(14(8)2)9-4-6-10(17-3)7-5-9/h4-8,11-13,15-16H,1-3H3/t8-,11-,12+,13-/m0/s1

IUPAC InChI key

GJZNAEFHIYPPEM-KNDHEWATSA-N
16Z

wwPDB Information

Atom count

36 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-03-08

Last modified at

2013-09-13

Status

Released

Obsoleted

Not Assigned



16Z : 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 CAA C CAA R N N 0 -2.939 -0.3 0.842
2 CAB C CAB N N N 0 -3.735 1.953 0.018
3 CAE C CAE S N N 0 -1.006 -0.397 -0.614
4 CAF C CAF S N N 0 -2.514 1.136 0.445
5 CAG C CAG S N N 0 -1.621 -1.089 0.62
6 CAI C CAI N N N 0 -0.539 1.982 -0.687
7 CAJ C CAJ N Y N 0 0.49 -0.302 -0.456
8 CAK C CAK N Y N 0 1.321 -0.75 -1.467
9 CAL C CAL N Y N 0 2.692 -0.658 -1.327
10 CAM C CAM N Y N 0 3.235 -0.128 -0.166
11 CAN C CAN N Y N 0 2.4 0.316 0.849
12 CAO C CAO N Y N 0 1.029 0.227 0.702
13 CAQ C CAQ N N N 0 5.073 0.52 1.196
14 H1 H H1 N N N 0 4.698 1.538 1.308
15 H10 H H10 N N N 0 -2.281 -2.945 1.089
16 H11 H H11 N N N 0 -3.247 -0.341 1.887
17 H12 H H12 N N N 0 -4.207 -1.71 0.132
18 H13 H H13 N N N 0 -2.003 1.624 1.275
19 H14 H H14 N N N 0 -4.443 2.008 0.845
20 H15 H H15 N N N 0 -3.42 2.96 -0.258
21 H16 H H16 N N N 0 -4.212 1.475 -0.837
22 H18 H H18 N N N 0 0.201 1.75 -1.453
23 H19 H H19 N N N 0 -0.982 2.956 -0.894
24 H2 H H2 N N N 0 4.732 -0.087 2.035
25 H20 H H20 N N N 0 -0.056 2.003 0.29
26 H3 H H3 N N N 0 6.163 0.535 1.178
27 H4 H H4 N N N 0 2.82 0.729 1.754
28 H5 H H5 N N N 0 0.378 0.572 1.492
29 H6 H H6 N N N 0 3.34 -1.0 -2.12
30 H7 H H7 N N N 0 0.897 -1.163 -2.37
31 H8 H H8 N N N 0 -1.248 -0.959 -1.517
32 H9 H H9 N N N 0 -0.964 -0.992 1.484
33 NAH N NAH N N N 0 -1.589 0.955 -0.693
34 OAC O OAC N N N 0 -3.975 -0.783 -0.015
35 OAD O OAD N N N 0 -1.893 -2.465 0.345
36 OAP O OAP N N N 0 4.584 -0.037 -0.025



16Z : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAC CAA O C sing 1.43 N N
2 OAD CAG O C sing 1.43 N N
3 CAA CAG C C sing 1.55 N N
4 CAA CAF C C sing 1.55 N N
5 CAG CAE C C sing 1.54 N N
6 CAE NAH C N sing 1.47 N N
7 CAE CAJ C C sing 1.51 N N
8 NAH CAF N C sing 1.48 N N
9 NAH CAI N C sing 1.47 N N
10 CAB CAF C C sing 1.53 N N
11 CAO CAJ C C doub 1.38 N Y
12 CAO CAN C C sing 1.38 N Y
13 CAJ CAK C C sing 1.38 N Y
14 CAN CAM C C doub 1.39 N Y
15 CAK CAL C C doub 1.38 N Y
16 CAM CAL C C sing 1.39 N Y
17 CAM OAP C O sing 1.36 N N
18 OAP CAQ O C sing 1.43 N N
19 CAQ H1 C H sing 1.09 N N
20 CAQ H2 C H sing 1.09 N N
21 CAQ H3 C H sing 1.09 N N
22 CAN H4 C H sing 1.08 N N
23 CAO H5 C H sing 1.08 N N
24 CAL H6 C H sing 1.08 N N
25 CAK H7 C H sing 1.08 N N
26 CAE H8 C H sing 1.09 N N
27 CAG H9 C H sing 1.09 N N
28 OAD H10 O H sing 0.97 N N
29 CAA H11 C H sing 1.09 N N
30 OAC H12 O H sing 0.97 N N
31 CAF H13 C H sing 1.09 N N
32 CAB H14 C H sing 1.09 N N
33 CAB H15 C H sing 1.09 N N
34 CAB H16 C H sing 1.09 N N
35 CAI H18 C H sing 1.09 N N
36 CAI H19 C H sing 1.09 N N
37 CAI H20 C H sing 1.09 N N



16Z : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
16Z 4jfs Open in New Window Bound ligand 2 1