Chemical Components in the PDB

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Y41 : Summary

Code

Y41

One-letter code

X

Molecule name

3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide

Systematic names

ProgramVersionName
ACDLabs 12.01 3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide
OpenEye OEToolkits 2.0.7 3-azanyl-2-methyl-~{N}-[(1~{R})-1-naphthalen-1-ylethyl]benzamide

Formula

C20 H20 N2 O

Formal charge

0

Molecular weight

304.386 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(c1cccc(N)c1C)NC(C)c2cccc3c2cccc3
SMILES CACTVS 3.385 C[CH](NC(=O)c1cccc(N)c1C)c2cccc3ccccc23
SMILES OpenEye OEToolkits 2.0.7 Cc1c(cccc1N)C(=O)NC(C)c2cccc3c2cccc3
Canonical SMILES CACTVS 3.385 C[C@@H](NC(=O)c1cccc(N)c1C)c2cccc3ccccc23
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1c(cccc1N)C(=O)N[C@H](C)c2cccc3c2cccc3

IUPAC InChI

InChI=1S/C20H20N2O/c1-13-16(10-6-12-19(13)21)20(23)22-14(2)17-11-5-8-15-7-3-4-9-18(15)17/h3-12,14H,21H2,1-2H3,(H,22,23)/t14-/m1/s1

IUPAC InChI key

PZEBTCMUWPLVEX-CQSZACIVSA-N
Y41

wwPDB Information

Atom count

43 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-08-04

Last modified at

2020-08-07

Status

Released

Obsoleted

Not Assigned



Y41 : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O7 O O1 N N N 0 1.452 -1.776 -0.326
2 C1 C C1 N N N 0 1.509 -0.562 -0.328
3 C3 C C2 N Y N 0 2.801 0.118 -0.09
4 C10 C C3 N Y N 0 2.898 1.504 -0.222
5 C17 C C4 N Y N 0 4.104 2.136 0.001
6 C21 C C5 N Y N 0 5.22 1.4 0.354
7 C19 C C6 N Y N 0 5.134 0.02 0.488
8 N01 N N1 N N N 0 6.265 -0.719 0.847
9 C13 C C7 N Y N 0 3.925 -0.624 0.272
10 C23 C C8 N N N 0 3.827 -2.12 0.423
11 N2 N N2 N N N 0 0.397 0.166 -0.553
12 C6 C C9 R N N 0 -0.882 -0.508 -0.795
13 C01 C C10 N N N 0 -1.018 -0.822 -2.286
14 C5 C C11 N Y N 0 -2.012 0.392 -0.366
15 C8 C C12 N Y N 0 -3.236 -0.161 0.047
16 C14 C C13 N Y N 0 -3.44 -1.551 0.066
17 C20 C C14 N Y N 0 -4.639 -2.05 0.472
18 C22 C C15 N Y N 0 -5.671 -1.203 0.872
19 C18 C C16 N Y N 0 -5.51 0.149 0.867
20 C11 C C17 N Y N 0 -4.286 0.701 0.453
21 C12 C C18 N Y N 0 -4.081 2.091 0.435
22 C9 C C19 N Y N 0 -2.882 2.591 0.029
23 C4 C C20 N Y N 0 -1.85 1.743 -0.37
24 H1 H H1 N N N 0 2.029 2.082 -0.499
25 H2 H H2 N N N 0 4.177 3.208 -0.102
26 H3 H H3 N N N 0 6.162 1.9 0.527
27 H4 H H4 N N N 0 7.109 -0.269 1.002
28 H5 H H5 N N N 0 6.205 -1.683 0.94
29 H7 H H7 N N N 0 4.619 -2.471 1.084
30 H6 H H6 N N N 0 3.934 -2.591 -0.554
31 H8 H H8 N N N 0 2.858 -2.38 0.848
32 H9 H H9 N N N 0 0.443 1.134 -0.555
33 H10 H H10 N N N 0 -0.918 -1.435 -0.224
34 H11 H H11 N N N 0 -0.201 -1.472 -2.597
35 H12 H H12 N N N 0 -1.97 -1.322 -2.466
36 H13 H H13 N N N 0 -0.982 0.106 -2.858
37 H14 H H14 N N N 0 -2.65 -2.22 -0.241
38 H15 H H15 N N N 0 -4.794 -3.119 0.485
39 H16 H H16 N N N 0 -6.613 -1.625 1.189
40 H17 H H17 N N N 0 -6.319 0.793 1.179
41 H18 H H18 N N N 0 -4.872 2.76 0.742
42 H19 H H19 N N N 0 -2.728 3.659 0.016
43 H20 H H20 N N N 0 -0.907 2.165 -0.683



Y41 : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C22 C18 C C doub 1.36 N Y
2 C22 C20 C C sing 1.39 N Y
3 C18 C11 C C sing 1.41 N Y
4 C20 C14 C C doub 1.36 N Y
5 C11 C12 C C doub 1.41 N Y
6 C11 C8 C C sing 1.42 N Y
7 C14 C8 C C sing 1.41 N Y
8 C12 C9 C C sing 1.36 N Y
9 C8 C5 C C doub 1.41 N Y
10 O7 C1 O C doub 1.22 N N
11 C23 C13 C C sing 1.51 N N
12 C9 C4 C C doub 1.39 N Y
13 C1 C3 C C sing 1.48 N N
14 C1 N2 C N sing 1.35 N N
15 C13 C3 C C doub 1.39 N Y
16 C13 C19 C C sing 1.39 N Y
17 N01 C19 N C sing 1.4 N N
18 C5 C4 C C sing 1.36 N Y
19 C5 C6 C C sing 1.51 N N
20 C3 C10 C C sing 1.4 N Y
21 C19 C21 C C doub 1.39 N Y
22 C10 C17 C C doub 1.38 N Y
23 C21 C17 C C sing 1.38 N Y
24 C6 N2 C N sing 1.47 N N
25 C6 C01 C C sing 1.53 N N
26 C10 H1 C H sing 1.08 N N
27 C17 H2 C H sing 1.08 N N
28 C21 H3 C H sing 1.08 N N
29 N01 H4 N H sing 0.97 N N
30 N01 H5 N H sing 0.97 N N
31 C23 H6 C H sing 1.09 N N
32 C23 H7 C H sing 1.09 N N
33 C23 H8 C H sing 1.09 N N
34 N2 H9 N H sing 0.97 N N
35 C6 H10 C H sing 1.09 N N
36 C01 H11 C H sing 1.09 N N
37 C01 H12 C H sing 1.09 N N
38 C01 H13 C H sing 1.09 N N
39 C14 H14 C H sing 1.08 N N
40 C20 H15 C H sing 1.08 N N
41 C22 H16 C H sing 1.08 N N
42 C18 H17 C H sing 1.08 N N
43 C12 H18 C H sing 1.08 N N
44 C9 H19 C H sing 1.08 N N
45 C4 H20 C H sing 1.08 N N



Y41 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
Y41 7jn2 Open in New Window Bound ligand 1 1
Y41 7krx Open in New Window Bound ligand 1 1