Chemical Components in the PDB

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DJU : Summary

Code

DJU

One-letter code

X

Molecule name

N,N-dimethyl-1-(5-phenylmethoxy-1H-indol-3-yl)methanamine

Synonyms

5-Benzyloxygramine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 ~{N},~{N}-dimethyl-1-(5-phenylmethoxy-1~{H}-indol-3-yl)methanamine

Formula

C18 H20 N2 O

Formal charge

0

Molecular weight

280.364 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN(C)Cc1c[nH]c2ccc(OCc3ccccc3)cc12
SMILES OpenEye OEToolkits 2.0.7 CN(C)Cc1c[nH]c2c1cc(cc2)OCc3ccccc3
Canonical SMILES CACTVS 3.385 CN(C)Cc1c[nH]c2ccc(OCc3ccccc3)cc12
Canonical SMILES OpenEye OEToolkits 2.0.7 CN(C)Cc1c[nH]c2c1cc(cc2)OCc3ccccc3

IUPAC InChI

InChI=1S/C18H20N2O/c1-20(2)12-15-11-19-18-9-8-16(10-17(15)18)21-13-14-6-4-3-5-7-14/h3-11,19H,12-13H2,1-2H3

IUPAC InChI key

POTVAILTNPOQJH-UHFFFAOYSA-N
DJU

wwPDB Information

Atom count

41 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-08-02

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



DJU : 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 CAD C C1 N Y N 0 -3.414 0.163 -0.524
2 CAE C C2 N Y N 0 -2.046 0.624 -0.274
3 CAF C C3 N Y N 0 -2.153 1.975 0.1
4 CAG C C4 N N N 0 -3.83 -1.22 -0.953
5 CAH C C5 N Y N 0 -4.228 1.205 -0.292
6 CAI C C6 N Y N 0 -0.791 0.014 -0.338
7 CAJ C C7 N Y N 0 -1.002 2.695 0.405
8 CAK C C8 N Y N 0 0.338 0.746 -0.032
9 CAL C C9 N Y N 0 0.23 2.084 0.338
10 CAM C C10 N N N 0 -4.894 -1.711 1.166
11 CAN C C11 N N N 0 -4.015 -3.512 -0.192
12 CAO C C12 N N N 0 2.691 0.971 0.237
13 CAP C C13 N Y N 0 3.952 0.155 0.116
14 CAQ C C14 N Y N 0 4.427 -0.55 1.206
15 CAR C C15 N Y N 0 4.63 0.106 -1.088
16 CAS C C16 N Y N 0 5.583 -1.298 1.095
17 CAT C C17 N Y N 0 5.787 -0.643 -1.199
18 CAU C C18 N Y N 0 6.265 -1.343 -0.107
19 NAB N N1 N Y N 0 -3.493 2.299 0.076
20 NAC N N2 N N N 0 -3.848 -2.111 0.216
21 OAA O O1 N N N 0 1.563 0.157 -0.092
22 HAH H H1 N N N 0 -4.825 -1.18 -1.394
23 HAG H H2 N N N 0 -3.121 -1.601 -1.688
24 HAI H H3 N N N 0 -5.304 1.184 -0.386
25 HAJ H H4 N N N 0 -0.706 -1.023 -0.625
26 HAK H H5 N N N 0 -1.075 3.734 0.692
27 HAL H H6 N N N 0 1.12 2.648 0.575
28 HAN H H7 N N N 0 -5.866 -1.757 0.676
29 HAM H H8 N N N 0 -4.885 -2.386 2.022
30 HAO H H9 N N N 0 -4.706 -0.692 1.506
31 HAQ H H10 N N N 0 -3.188 -3.803 -0.841
32 HAP H H11 N N N 0 -4.025 -4.149 0.692
33 HAR H H12 N N N 0 -4.956 -3.623 -0.731
34 HAS H H13 N N N 0 2.59 1.335 1.26
35 HAT H H14 N N N 0 2.739 1.819 -0.447
36 HAU H H15 N N N 0 3.894 -0.515 2.145
37 HAV H H16 N N N 0 4.256 0.653 -1.941
38 HAW H H17 N N N 0 5.955 -1.848 1.947
39 HAX H H18 N N N 0 6.317 -0.681 -2.139
40 HAY H H19 N N N 0 7.169 -1.928 -0.194
41 HAB H H20 N N N 0 -3.861 3.17 0.292



DJU : 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 CAJ CAL C C doub 1.38 N Y
2 CAJ CAF C C sing 1.39 N Y
3 CAL CAK C C sing 1.39 N Y
4 NAB CAF N C sing 1.38 N Y
5 NAB CAH N C sing 1.37 N Y
6 CAF CAE C C doub 1.41 N Y
7 CAK OAA C O sing 1.36 N N
8 CAK CAI C C doub 1.38 N Y
9 CAH CAD C C doub 1.34 N Y
10 OAA CAO O C sing 1.43 N N
11 CAE CAI C C sing 1.4 N Y
12 CAE CAD C C sing 1.47 N Y
13 CAD CAG C C sing 1.51 N N
14 CAG NAC C N sing 1.47 N N
15 CAO CAP C C sing 1.51 N N
16 CAQ CAP C C doub 1.38 N Y
17 CAQ CAS C C sing 1.38 N Y
18 CAP CAR C C sing 1.38 N Y
19 NAC CAN N C sing 1.47 N N
20 NAC CAM N C sing 1.47 N N
21 CAS CAU C C doub 1.38 N Y
22 CAR CAT C C doub 1.38 N Y
23 CAU CAT C C sing 1.38 N Y
24 CAG HAH C H sing 1.09 N N
25 CAG HAG C H sing 1.09 N N
26 CAH HAI C H sing 1.08 N N
27 CAI HAJ C H sing 1.08 N N
28 CAJ HAK C H sing 1.08 N N
29 CAL HAL C H sing 1.08 N N
30 CAM HAN C H sing 1.09 N N
31 CAM HAM C H sing 1.09 N N
32 CAM HAO C H sing 1.09 N N
33 CAN HAQ C H sing 1.09 N N
34 CAN HAP C H sing 1.09 N N
35 CAN HAR C H sing 1.09 N N
36 CAO HAS C H sing 1.09 N N
37 CAO HAT C H sing 1.09 N N
38 CAQ HAU C H sing 1.08 N N
39 CAR HAV C H sing 1.08 N N
40 CAS HAW C H sing 1.08 N N
41 CAT HAX C H sing 1.08 N N
42 CAU HAY C H sing 1.08 N N
43 NAB HAB N H sing 0.97 N N



DJU : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
DJU 6kl6 Open in New Window Bound ligand 1 1
DJU 8iv3 Open in New Window Bound ligand 1 1