Chemical Components in the PDB

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21B : Summary

Code

21B

One-letter code

X

Molecule name

Nortriptyline

Synonyms

3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N-methylpropan-1-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N-methylpropan-1-amine
OpenEye OEToolkits 1.7.6 3-(5,6-dihydrodibenzo[1,2-a:1',2'-e][7]annulen-11-ylidene)-N-methyl-propan-1-amine

Formula

C19 H21 N

Formal charge

0

Molecular weight

263.377 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c3cc2c(/C(c1c(cccc1)CC2)=C/CCNC)cc3
SMILES CACTVS 3.385 CNCCC=C1c2ccccc2CCc3ccccc13
SMILES OpenEye OEToolkits 1.7.6 CNCCC=C1c2ccccc2CCc3c1cccc3
Canonical SMILES CACTVS 3.385 CNCCC=C1c2ccccc2CCc3ccccc13
Canonical SMILES OpenEye OEToolkits 1.7.6 CNCCC=C1c2ccccc2CCc3c1cccc3

IUPAC InChI

InChI=1S/C19H21N/c1-20-14-6-11-19-17-9-4-2-7-15(17)12-13-16-8-3-5-10-18(16)19/h2-5,7-11,20H,6,12-14H2,1H3

IUPAC InChI key

PHVGLTMQBUFIQQ-UHFFFAOYSA-N
21B

wwPDB Information

Atom count

41 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-08-14

Last modified at

2013-09-13

Status

Released

Obsoleted

Not Assigned



21B : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C16 C C16 N N N 0 5.116 2.334 -1.111
2 N N N N N N 0 4.354 1.444 -0.225
3 C15 C C15 N N N 0 2.936 1.826 -0.187
4 C14 C C14 N N N 0 2.177 0.879 0.744
5 C13 C C13 N N N 0 0.722 1.271 0.782
6 C4 C C4 N N N 0 -0.223 0.359 0.528
7 C3 C C3 N Y N 0 0.161 -1.063 0.39
8 C17 C C17 N Y N 0 1.07 -1.552 1.342
9 C18 C C18 N Y N 0 1.466 -2.869 1.327
10 C C C N Y N 0 0.953 -3.719 0.363
11 C5 C C5 N Y N 0 -1.632 0.793 0.396
12 C10 C C10 N Y N 0 -2.31 1.389 1.456
13 C9 C C9 N Y N 0 -3.623 1.782 1.274
14 C8 C C8 N Y N 0 -4.242 1.581 0.053
15 C7 C C7 N Y N 0 -3.561 0.985 -0.994
16 C6 C C6 N Y N 0 -2.246 0.586 -0.814
17 C11 C C11 N N N 0 -1.503 -0.079 -1.932
18 C12 C C12 N N N 0 -1.289 -1.551 -1.71
19 C2 C C2 N Y N 0 -0.338 -1.902 -0.586
20 C1 C C1 N Y N 0 0.067 -3.241 -0.575
21 H1 H H1 N N N 0 6.162 2.029 -1.12
22 H2 H H2 N N N 0 4.711 2.274 -2.121
23 H3 H H3 N N N 0 5.04 3.36 -0.749
24 H4 H H4 N N N 0 4.462 0.48 -0.501
25 H6 H H6 N N N 0 2.845 2.848 0.181
26 H7 H H7 N N N 0 2.516 1.763 -1.191
27 H8 H H8 N N N 0 2.269 -0.143 0.376
28 H9 H H9 N N N 0 2.597 0.942 1.748
29 H10 H H10 N N N 0 0.443 2.288 1.014
30 H11 H H11 N N N 0 1.463 -0.886 2.095
31 H12 H H12 N N N 0 2.171 -3.236 2.059
32 H13 H H13 N N N 0 1.247 -4.758 0.347
33 H14 H H14 N N N 0 -1.818 1.541 2.405
34 H15 H H15 N N N 0 -4.166 2.245 2.085
35 H16 H H16 N N N 0 -5.267 1.892 -0.085
36 H17 H H17 N N N 0 -4.051 0.832 -1.944
37 H18 H H18 N N N 0 -2.065 0.058 -2.856
38 H19 H H19 N N N 0 -0.531 0.402 -2.04
39 H20 H H20 N N N 0 -2.256 -2.007 -1.496
40 H21 H H21 N N N 0 -0.906 -1.986 -2.633
41 H22 H H22 N N N 0 -0.325 -3.916 -1.321



21B : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C16 N C N sing 1.47 N N
2 N C15 N C sing 1.47 N N
3 C1 C C C doub 1.38 N Y
4 C1 C2 C C sing 1.4 N Y
5 C12 C2 C C sing 1.51 N N
6 C12 C11 C C sing 1.5 N N
7 C C18 C C sing 1.38 N Y
8 C2 C3 C C doub 1.38 N Y
9 C15 C14 C C sing 1.53 N N
10 C18 C17 C C doub 1.38 N Y
11 C13 C14 C C sing 1.51 N N
12 C13 C4 C C doub 1.34 N N
13 C3 C17 C C sing 1.4 N Y
14 C3 C4 C C sing 1.48 N N
15 C11 C6 C C sing 1.5 N N
16 C4 C5 C C sing 1.48 N N
17 C6 C5 C C doub 1.37 N Y
18 C6 C7 C C sing 1.39 N Y
19 C5 C10 C C sing 1.39 N Y
20 C7 C8 C C doub 1.38 N Y
21 C10 C9 C C doub 1.38 N Y
22 C8 C9 C C sing 1.38 N Y
23 C16 H1 C H sing 1.09 N N
24 C16 H2 C H sing 1.09 N N
25 C16 H3 C H sing 1.09 N N
26 N H4 N H sing 1.01 N N
27 C15 H6 C H sing 1.09 N N
28 C15 H7 C H sing 1.09 N N
29 C14 H8 C H sing 1.09 N N
30 C14 H9 C H sing 1.09 N N
31 C13 H10 C H sing 1.08 N N
32 C17 H11 C H sing 1.08 N N
33 C18 H12 C H sing 1.08 N N
34 C H13 C H sing 1.08 N N
35 C10 H14 C H sing 1.08 N N
36 C9 H15 C H sing 1.08 N N
37 C8 H16 C H sing 1.08 N N
38 C7 H17 C H sing 1.08 N N
39 C11 H18 C H sing 1.09 N N
40 C11 H19 C H sing 1.09 N N
41 C12 H20 C H sing 1.09 N N
42 C12 H21 C H sing 1.09 N N
43 C1 H22 C H sing 1.08 N N



21B : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
21B 4m48 Open in New Window Bound ligand 1 1