Chemical Components in the PDB

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1KN : Summary

Code

1KN

One-letter code

X

Molecule name

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

Synonyms

N-desmethyl-4-epi-(+)-Codonopsinine

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S,3S,4R,5S)-2-(4-methoxyphenyl)-5-methylpyrrolidine-3,4-diol
OpenEye OEToolkits 1.7.6 (2S,3S,4R,5S)-2-(4-methoxyphenyl)-5-methyl-pyrrolidine-3,4-diol

Formula

C12 H17 N O3

Formal charge

0

Molecular weight

223.268 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC2C(c1ccc(OC)cc1)NC(C)C2O
SMILES CACTVS 3.370 COc1ccc(cc1)[CH]2N[CH](C)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.7.6 CC1C(C(C(N1)c2ccc(cc2)OC)O)O
Canonical SMILES CACTVS 3.370 COc1ccc(cc1)[C@@H]2N[C@@H](C)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H]1[C@H]([C@H]([C@@H](N1)c2ccc(cc2)OC)O)O

IUPAC InChI

InChI=1S/C12H17NO3/c1-7-11(14)12(15)10(13-7)8-3-5-9(16-2)6-4-8/h3-7,10-15H,1-2H3/t7-,10-,11+,12-/m0/s1

IUPAC InChI key

RMKWLQBEDHKISQ-VKZDFBPFSA-N
1KN

wwPDB Information

Atom count

33 (16 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



1KN : 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 CAA C CAA R N N 0 -3.046 0.222 -0.698
2 CAB C CAB S N N 0 -1.664 0.924 -0.642
3 CAC C CAC S N N 0 -0.994 0.276 0.587
4 CAE C CAE S N N 0 -2.688 -1.21 -0.23
5 CAF C CAF N N N 0 -3.92 -1.905 0.356
6 CAI C CAI N Y N 0 0.473 0.059 0.317
7 CAJ C CAJ N Y N 0 1.407 0.94 0.832
8 CAK C CAK N Y N 0 2.752 0.743 0.585
9 CAL C CAL N Y N 0 3.166 -0.344 -0.17
10 CAM C CAM N Y N 0 2.227 -1.232 -0.676
11 CAN C CAN N Y N 0 0.883 -1.029 -0.431
12 CAP C CAP N N N 0 5.398 0.412 0.143
13 H1 H H1 N N N 0 5.295 0.426 1.228
14 H11 H H11 N N N 0 -2.285 -1.791 -1.059
15 H12 H H12 N N N 0 -4.32 -1.306 1.174
16 H13 H H13 N N N 0 -4.678 -2.014 -0.419
17 H14 H H14 N N N 0 -3.638 -2.889 0.73
18 H15 H H15 N N N 0 -3.439 0.214 -1.715
19 H16 H H16 N N N 0 -4.15 1.768 0.0030
20 H17 H H17 N N N 0 -1.091 0.72 -1.546
21 H18 H H18 N N N 0 -2.303 2.775 -1.16
22 H2 H H2 N N N 0 6.419 0.136 -0.122
23 H3 H H3 N N N 0 5.173 1.401 -0.256
24 H4 H H4 N N N 0 2.548 -2.082 -1.261
25 H5 H H5 N N N 0 0.153 -1.719 -0.824
26 H6 H H6 N N N 0 3.48 1.436 0.98
27 H7 H H7 N N N 0 1.083 1.789 1.416
28 H8 H H8 N N N 0 -1.12 0.915 1.461
29 H9 H H9 N N N 0 -0.991 -1.776 0.805
30 NAD N NAD N N N 0 -1.659 -1.02 0.814
31 OAG O OAG N N N 0 -1.82 2.332 -0.449
32 OAH O OAH N N N 0 -3.97 0.839 0.2
33 OAO O OAO N N N 0 4.489 -0.543 -0.409



1KN : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAH CAA O C sing 1.43 N N
2 OAG CAB O C sing 1.43 N N
3 CAA CAB C C sing 1.55 N N
4 CAA CAE C C sing 1.55 N N
5 CAB CAC C C sing 1.54 N N
6 CAC NAD C N sing 1.47 N N
7 CAC CAI C C sing 1.51 N N
8 CAF CAE C C sing 1.53 N N
9 NAD CAE N C sing 1.48 N N
10 CAJ CAI C C doub 1.38 N Y
11 CAJ CAK C C sing 1.38 N Y
12 CAI CAN C C sing 1.38 N Y
13 CAK CAL C C doub 1.39 N Y
14 CAN CAM C C doub 1.38 N Y
15 CAL CAM C C sing 1.39 N Y
16 CAL OAO C O sing 1.36 N N
17 OAO CAP O C sing 1.43 N N
18 CAP H1 C H sing 1.09 N N
19 CAP H2 C H sing 1.09 N N
20 CAP H3 C H sing 1.09 N N
21 CAM H4 C H sing 1.08 N N
22 CAN H5 C H sing 1.08 N N
23 CAK H6 C H sing 1.08 N N
24 CAJ H7 C H sing 1.08 N N
25 CAC H8 C H sing 1.09 N N
26 NAD H9 N H sing 1.01 N N
27 CAE H11 C H sing 1.09 N N
28 CAF H12 C H sing 1.09 N N
29 CAF H13 C H sing 1.09 N N
30 CAF H14 C H sing 1.09 N N
31 CAA H15 C H sing 1.09 N N
32 OAH H16 O H sing 0.97 N N
33 CAB H17 C H sing 1.09 N N
34 OAG H18 O H sing 0.97 N N



1KN : Used in PDB Entries

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