Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

LDV : Summary

Code

LDV

One-letter code

X

Molecule name

3-[(4-methylpiperidin-1-yl)methyl]-1H-indole

Systematic names

ProgramVersionName
ACDLabs 12.01 3-[(4-methylpiperidin-1-yl)methyl]-1H-indole
OpenEye OEToolkits 2.0.6 3-[(4-methylpiperidin-1-yl)methyl]-1~{H}-indole

Formula

C15 H20 N2

Formal charge

0

Molecular weight

228.333 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N1(CCC(CC1)C)Cc3c2c(cccc2)nc3
SMILES CACTVS 3.385 CC1CCN(CC1)Cc2c[nH]c3ccccc23
SMILES OpenEye OEToolkits 2.0.6 CC1CCN(CC1)Cc2c[nH]c3c2cccc3
Canonical SMILES CACTVS 3.385 CC1CCN(CC1)Cc2c[nH]c3ccccc23
Canonical SMILES OpenEye OEToolkits 2.0.6 CC1CCN(CC1)Cc2c[nH]c3c2cccc3

IUPAC InChI

InChI=1S/C15H20N2/c1-12-6-8-17(9-7-12)11-13-10-16-15-5-3-2-4-14(13)15/h2-5,10,12,16H,6-9,11H2,1H3

IUPAC InChI key

DGCGMYNLCDVYMB-UHFFFAOYSA-N
LDV

wwPDB Information

Atom count

37 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-02-22

Last modified at

2019-05-03

Status

Released

Obsoleted

Not Assigned



LDV : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -1.399 0.219 0.465
2 C4 C C1 N N N 0 -2.546 0.877 1.103
3 C5 C C2 N N N 0 -1.837 -0.856 -0.435
4 C6 C C3 N N N 0 -2.7 -0.268 -1.553
5 C7 C C4 N N N 0 -0.455 -0.287 1.47
6 C8 C C5 N Y N 0 0.814 -0.731 0.79
7 C10 C C6 N Y N 0 2.868 -0.725 -0.232
8 C13 C C7 N Y N 0 3.294 2.018 -0.144
9 C1 C C9 N N N 0 -4.766 -0.586 -0.181
10 C11 C C10 N Y N 0 1.909 0.132 0.339
11 C12 C C11 N Y N 0 2.138 1.508 0.376
12 C14 C C12 N Y N 0 4.244 1.177 -0.708
13 C2 C C13 N N N 0 -3.914 0.434 -0.938
14 C3 C C14 N N N 0 -3.431 1.517 0.031
15 C9 C C15 N Y N 0 1.158 -1.993 0.486
16 N2 N N2 N Y N 0 2.381 -2.008 -0.126
17 H2 H H2 N N N 0 -3.125 0.139 1.659
18 H3 H H3 N N N 0 -2.189 1.648 1.786
19 H4 H H4 N N N 0 -0.964 -1.344 -0.869
20 H5 H H5 N N N 0 -2.419 -1.586 0.128
21 H6 H H6 N N N 0 -2.115 0.452 -2.125
22 H7 H H7 N N N 0 -3.038 -1.068 -2.211
23 H8 H H8 N N N 0 -0.227 0.504 2.185
24 H9 H H9 N N N 0 -0.902 -1.132 1.994
25 H10 H H10 N N N 0 3.47 3.083 -0.115
26 H11 H H11 N N N 0 4.784 -0.83 -1.196
27 H12 H H12 N N N 0 -4.17 -1.041 0.611
28 H13 H H13 N N N 0 -5.63 -0.086 0.257
29 H14 H H14 N N N 0 -5.105 -1.36 -0.87
30 H15 H H15 N N N 0 1.403 2.168 0.813
31 H16 H H16 N N N 0 5.153 1.595 -1.115
32 H17 H H17 N N N 0 -4.51 0.891 -1.728
33 H18 H H18 N N N 0 -4.291 1.992 0.504
34 H19 H H19 N N N 0 -2.857 2.265 -0.516
35 H20 H H20 N N N 0 0.557 -2.866 0.693
36 H21 H H21 N N N 0 2.839 -2.805 -0.437
37 C15 C C8 N Y N 0 4.038 -0.184 -0.755



LDV : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C6 C2 C C sing 1.53 N N
3 C6 C5 C C sing 1.53 N N
4 C2 C3 C C sing 1.53 N N
5 C5 N1 C N sing 1.47 N N
6 C3 C4 C C sing 1.53 N N
7 C9 N2 C N sing 1.37 N Y
8 C9 C8 C C doub 1.34 N Y
9 N2 C10 N C sing 1.38 N Y
10 N1 C4 N C sing 1.47 N N
11 N1 C7 N C sing 1.47 N N
12 C8 C7 C C sing 1.51 N N
13 C8 C11 C C sing 1.47 N Y
14 C10 C11 C C doub 1.41 N Y
15 C10 C15 C C sing 1.39 N Y
16 C11 C12 C C sing 1.4 N Y
17 C15 C14 C C doub 1.38 N Y
18 C14 C13 C C sing 1.39 N Y
19 C12 C13 C C doub 1.37 N Y
20 C4 H2 C H sing 1.09 N N
21 C4 H3 C H sing 1.09 N N
22 C5 H4 C H sing 1.09 N N
23 C5 H5 C H sing 1.09 N N
24 C6 H6 C H sing 1.09 N N
25 C6 H7 C H sing 1.09 N N
26 C7 H8 C H sing 1.09 N N
27 C7 H9 C H sing 1.09 N N
28 C13 H10 C H sing 1.08 N N
29 C15 H11 C H sing 1.08 N N
30 C1 H12 C H sing 1.09 N N
31 C1 H13 C H sing 1.09 N N
32 C1 H14 C H sing 1.09 N N
33 C12 H15 C H sing 1.08 N N
34 C14 H16 C H sing 1.08 N N
35 C2 H17 C H sing 1.09 N N
36 C3 H18 C H sing 1.09 N N
37 C3 H19 C H sing 1.09 N N
38 C9 H20 C H sing 1.08 N N
39 N2 H21 N H sing 0.97 N N



LDV : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
LDV 5qom Open in New Window Bound ligand 1 1
LDV 5qpn Open in New Window Bound ligand 1 1
LDV 5sdc Open in New Window Bound ligand 2 1