Chemical Components in the PDB

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RND : Summary

Code

RND

One-letter code

X

Molecule name

N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-3-(1H-indol-3-yl)-N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]propanamide

Formula

C25 H29 N5 O

Formal charge

0

Molecular weight

415.531 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC3CCN(Cc1cnc2ccccc12)CC3)C(N)Cc5c4ccccc4nc5
SMILES CACTVS 3.385 N[CH](Cc1c[nH]c2ccccc12)C(=O)NC3CCN(CC3)Cc4c[nH]c5ccccc45
SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)c(c[nH]2)CC(C(=O)NC3CCN(CC3)Cc4c[nH]c5c4cccc5)N
Canonical SMILES CACTVS 3.385 N[C@@H](Cc1c[nH]c2ccccc12)C(=O)NC3CCN(CC3)Cc4c[nH]c5ccccc45
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NC3CCN(CC3)Cc4c[nH]c5c4cccc5)N

IUPAC InChI

InChI=1S/C25H29N5O/c26-22(13-17-14-27-23-7-3-1-5-20(17)23)25(31)29-19-9-11-30(12-10-19)16-18-15-28-24-8-4-2-6-21(18)24/h1-8,14-15,19,22,27-28H,9-13,16,26H2,(H,29,31)/t22-/m0/s1

IUPAC InChI key

YLGBZXMOCLUOKZ-QFIPXVFZSA-N
RND

wwPDB Information

Atom count

60 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-12-25

Last modified at

2014-03-07

Status

Released

Obsoleted

Not Assigned



RND : Atoms of Molecule

Total Number of Atoms: 60
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N Y N 0 -6.444 0.171 -0.631
2 C02 C C02 N Y N 0 -7.722 0.203 -0.149
3 C03 C C03 N Y N 0 -8.154 -0.744 0.77
4 C04 C C04 N Y N 0 -7.302 -1.732 1.212
5 C05 C C05 N Y N 0 -5.996 -1.784 0.735
6 C06 C C06 N Y N 0 -5.566 -0.825 -0.2
7 N07 N N07 N Y N 0 -4.932 -2.623 0.976
8 C08 C C08 N Y N 0 -4.168 -1.148 -0.497
9 C09 C C09 N Y N 0 -3.851 -2.228 0.235
10 C10 C C10 N N N 0 -3.26 -0.41 -1.446
11 N11 N N11 N N N 0 -2.738 0.794 -0.787
12 C12 C C12 N N N 0 -2.043 1.661 -1.747
13 C13 C C13 N N N 0 -1.641 2.968 -1.06
14 C14 C C14 N N N 0 -0.727 2.654 0.127
15 C15 C C15 N N N 0 -1.457 1.712 1.089
16 C16 C C16 N N N 0 -1.863 0.441 0.339
17 N17 N N17 N N N 0 0.498 2.01 -0.354
18 C18 C C18 N N N 0 1.631 2.091 0.37
19 C19 C C19 S N N 0 2.891 1.429 -0.125
20 O20 O O20 N N N 0 1.638 2.697 1.421
21 C21 C C21 N N N 0 2.84 -0.067 0.193
22 N22 N N22 N N N 0 4.055 2.031 0.539
23 C23 C C23 N Y N 0 4.04 -0.75 -0.409
24 N24 N N24 N Y N 0 5.349 -1.87 -1.809
25 C25 C C25 N Y N 0 4.094 -1.368 -1.6
26 C26 C C26 N Y N 0 5.372 -0.861 0.191
27 C27 C C27 N Y N 0 6.156 -1.577 -0.732
28 C28 C C28 N Y N 0 7.488 -1.843 -0.433
29 C29 C C29 N Y N 0 8.023 -1.403 0.757
30 C30 C C30 N Y N 0 7.246 -0.696 1.665
31 C31 C C31 N Y N 0 5.935 -0.424 1.391
32 H1 H H1 N N N 0 -6.116 0.911 -1.346
33 H2 H H2 N N N 0 -8.403 0.971 -0.486
34 H3 H H3 N N N 0 -9.167 -0.706 1.141
35 H4 H H4 N N N 0 -7.647 -2.464 1.927
36 H5 H H5 N N N 0 -4.946 -3.382 1.58
37 H6 H H6 N N N 0 -2.887 -2.714 0.238
38 H7 H H7 N N N 0 -2.43 -1.057 -1.731
39 H8 H H8 N N N 0 -3.819 -0.124 -2.336
40 H10 H H10 N N N 0 -1.15 1.154 -2.114
41 H11 H H11 N N N 0 -2.705 1.879 -2.585
42 H12 H H12 N N N 0 -1.112 3.604 -1.769
43 H13 H H13 N N N 0 -2.535 3.482 -0.706
44 H14 H H14 N N N 0 -0.472 3.579 0.645
45 H15 H H15 N N N 0 -0.795 1.451 1.915
46 H16 H H16 N N N 0 -2.347 2.207 1.477
47 H17 H H17 N N N 0 -2.396 -0.226 1.017
48 H18 H H18 N N N 0 -0.971 -0.06 -0.037
49 H19 H H19 N N N 0 0.493 1.526 -1.194
50 H20 H H20 N N N 0 2.975 1.568 -1.203
51 H21 H H21 N N N 0 2.845 -0.209 1.274
52 H22 H H22 N N N 0 1.929 -0.496 -0.225
53 H23 H H23 N N N 0 4.0 1.915 1.54
54 H24 H H24 N N N 0 4.916 1.649 0.177
55 H26 H H26 N N N 0 5.63 -2.358 -2.599
56 H27 H H27 N N N 0 3.268 -1.456 -2.29
57 H28 H H28 N N N 0 8.101 -2.392 -1.133
58 H29 H H29 N N N 0 9.058 -1.609 0.987
59 H30 H H30 N N N 0 7.681 -0.358 2.594
60 H31 H H31 N N N 0 5.336 0.126 2.102



RND : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C15 C16 C C sing 1.53 N N
2 C15 C14 C C sing 1.53 N N
3 N22 C19 N C sing 1.47 N N
4 C16 N11 C N sing 1.47 N N
5 C30 C31 C C doub 1.37 N Y
6 C30 C29 C C sing 1.39 N Y
7 C14 N17 C N sing 1.47 N N
8 C14 C13 C C sing 1.53 N N
9 N17 C18 N C sing 1.35 N N
10 C31 C26 C C sing 1.4 N Y
11 C18 C19 C C sing 1.51 N N
12 C18 O20 C O doub 1.21 N N
13 C19 C21 C C sing 1.53 N N
14 C29 C28 C C doub 1.38 N Y
15 N11 C10 N C sing 1.47 N N
16 N11 C12 N C sing 1.47 N N
17 C10 C08 C C sing 1.51 N N
18 C13 C12 C C sing 1.53 N N
19 C26 C23 C C sing 1.47 N Y
20 C26 C27 C C doub 1.41 N Y
21 C21 C23 C C sing 1.51 N N
22 C09 C08 C C doub 1.34 N Y
23 C09 N07 C N sing 1.37 N Y
24 C08 C06 C C sing 1.47 N Y
25 C28 C27 C C sing 1.39 N Y
26 C23 C25 C C doub 1.34 N Y
27 C27 N24 C N sing 1.38 N Y
28 N07 C05 N C sing 1.38 N Y
29 C06 C05 C C doub 1.41 N Y
30 C06 C01 C C sing 1.4 N Y
31 C25 N24 C N sing 1.37 N Y
32 C05 C04 C C sing 1.39 N Y
33 C01 C02 C C doub 1.37 N Y
34 C04 C03 C C doub 1.38 N Y
35 C02 C03 C C sing 1.39 N Y
36 C01 H1 C H sing 1.08 N N
37 C02 H2 C H sing 1.08 N N
38 C03 H3 C H sing 1.08 N N
39 C04 H4 C H sing 1.08 N N
40 N07 H5 N H sing 0.97 N N
41 C09 H6 C H sing 1.08 N N
42 C10 H7 C H sing 1.09 N N
43 C10 H8 C H sing 1.09 N N
44 C12 H10 C H sing 1.09 N N
45 C12 H11 C H sing 1.09 N N
46 C13 H12 C H sing 1.09 N N
47 C13 H13 C H sing 1.09 N N
48 C14 H14 C H sing 1.09 N N
49 C15 H15 C H sing 1.09 N N
50 C15 H16 C H sing 1.09 N N
51 C16 H17 C H sing 1.09 N N
52 C16 H18 C H sing 1.09 N N
53 N17 H19 N H sing 0.97 N N
54 C19 H20 C H sing 1.09 N N
55 C21 H21 C H sing 1.09 N N
56 C21 H22 C H sing 1.09 N N
57 N22 H23 N H sing 1.01 N N
58 N22 H24 N H sing 1.01 N N
59 N24 H26 N H sing 0.97 N N
60 C25 H27 C H sing 1.08 N N
61 C28 H28 C H sing 1.08 N N
62 C29 H29 C H sing 1.08 N N
63 C30 H30 C H sing 1.08 N N
64 C31 H31 C H sing 1.08 N N



RND : Used in PDB Entries

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