Chemical Components in the PDB

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GYX : Summary

Code

GYX

One-letter code

X

Molecule name

N-[(3-acetamidophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 ~{N}-[(3-acetamidophenyl)methyl]-1-[(1~{R})-1-naphthalen-1-ylethyl]piperidine-4-carboxamide

Formula

C27 H31 N3 O2

Formal charge

0

Molecular weight

429.554 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH](N1CCC(CC1)C(=O)NCc2cccc(NC(C)=O)c2)c3cccc4ccccc34
SMILES OpenEye OEToolkits 2.0.7 CC(c1cccc2c1cccc2)N3CCC(CC3)C(=O)NCc4cccc(c4)NC(=O)C
Canonical SMILES CACTVS 3.385 C[C@@H](N1CCC(CC1)C(=O)NCc2cccc(NC(C)=O)c2)c3cccc4ccccc34
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H](c1cccc2c1cccc2)N3CCC(CC3)C(=O)NCc4cccc(c4)NC(=O)C

IUPAC InChI

InChI=1S/C27H31N3O2/c1-19(25-12-6-9-22-8-3-4-11-26(22)25)30-15-13-23(14-16-30)27(32)28-18-21-7-5-10-24(17-21)29-20(2)31/h3-12,17,19,23H,13-16,18H2,1-2H3,(H,28,32)(H,29,31)/t19-/m1/s1

IUPAC InChI key

YQRGVYYHRJBSOR-LJQANCHMSA-N
GYX

wwPDB Information

Atom count

63 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-10-09

Last modified at

2020-10-30

Status

Released

Obsoleted

Not Assigned



GYX : Atoms of Molecule

Total Number of Atoms: 63
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C19 C C1 N Y N 0 4.911 -0.616 -0.587
2 C21 C C2 N N N 0 -0.545 3.521 0.031
3 C22 C C3 N N N 0 -1.644 2.802 -0.755
4 C23 C C4 N Y N 0 -4.201 0.314 0.387
5 C24 C C5 N Y N 0 -4.098 0.484 1.734
6 C25 C C6 N Y N 0 -4.736 -0.384 2.617
7 C26 C C7 N Y N 0 -5.483 -1.426 2.159
8 C27 C C8 N Y N 0 -5.613 -1.633 0.775
9 C10 C C9 N Y N 0 3.594 -0.964 -0.819
10 C11 C C10 N Y N 0 3.156 -2.245 -0.539
11 C12 C C11 N Y N 0 4.035 -3.182 -0.027
12 C13 C C12 N Y N 0 5.352 -2.841 0.206
13 C14 C C13 N Y N 0 5.795 -1.555 -0.073
14 C16 C C14 N N N 0 7.445 0.047 0.538
15 C17 C C15 N N N 0 8.89 0.454 0.671
16 C01 C C16 N N N 0 -4.475 2.362 -0.985
17 C02 C C17 R N N 0 -3.502 1.263 -0.552
18 C04 C C18 N N N 0 -1.444 0.838 0.65
19 C05 C C19 N N N 0 -0.339 1.498 1.477
20 C06 C C20 N N N 0 0.431 2.486 0.596
21 C07 C C21 N N N 0 1.09 1.743 -0.537
22 C09 C C22 N N N 0 2.633 0.055 -1.377
23 C28 C C23 N Y N 0 -4.958 -0.754 -0.123
24 C29 C C24 N Y N 0 -5.089 -0.961 -1.507
25 C30 C C25 N Y N 0 -5.839 -1.999 -1.965
26 C31 C C26 N Y N 0 -6.483 -2.864 -1.081
27 C32 C C27 N Y N 0 -6.375 -2.698 0.265
28 N03 N N1 N N N 0 -2.351 1.869 0.132
29 N08 N N2 N N N 0 1.993 0.777 -0.275
30 N15 N N3 N N N 0 7.131 -1.207 0.157
31 O18 O O1 N N N 0 6.565 0.847 0.775
32 O20 O O2 N N N 0 0.807 2.013 -1.685
33 H1 H H1 N N N 0 5.253 0.384 -0.81
34 H2 H H2 N N N 0 -0.01 4.202 -0.631
35 H3 H H3 N N N 0 -0.992 4.085 0.849
36 H4 H H4 N N N 0 -2.349 3.536 -1.147
37 H5 H H5 N N N 0 -1.198 2.25 -1.582
38 H6 H H6 N N N 0 -3.511 1.303 2.123
39 H7 H H7 N N N 0 -4.638 -0.227 3.681
40 H8 H H8 N N N 0 -5.975 -2.089 2.856
41 H9 H H9 N N N 0 2.126 -2.514 -0.721
42 H10 H H10 N N N 0 3.69 -4.182 0.191
43 H11 H H11 N N N 0 6.038 -3.574 0.607
44 H12 H H12 N N N 0 9.39 0.338 -0.291
45 H13 H H13 N N N 0 8.946 1.496 0.986
46 H17 H H17 N N N 0 -3.969 3.048 -1.664
47 H14 H H14 N N N 0 9.378 -0.177 1.413
48 H15 H H15 N N N 0 -5.328 1.912 -1.492
49 H16 H H16 N N N 0 -4.82 2.908 -0.107
50 H18 H H18 N N N 0 -3.157 0.717 -1.43
51 H19 H H19 N N N 0 -0.998 0.295 -0.184
52 H20 H H20 N N N 0 -2.003 0.144 1.278
53 H21 H H21 N N N 0 -0.783 2.03 2.319
54 H22 H H22 N N N 0 0.344 0.733 1.849
55 H23 H H23 N N N 0 1.191 2.99 1.193
56 H24 H H24 N N N 0 3.177 0.76 -2.007
57 H25 H H25 N N N 0 1.872 -0.451 -1.971
58 H26 H H26 N N N 0 -4.596 -0.298 -2.204
59 H27 H H27 N N N 0 -5.938 -2.156 -3.029
60 H28 H H28 N N N 0 -7.069 -3.683 -1.471
61 H29 H H29 N N N 0 -6.879 -3.376 0.938
62 H31 H H31 N N N 0 2.219 0.561 0.643
63 H32 H H32 N N N 0 7.831 -1.869 0.042



GYX : Chemical Bonds

Total Number of Bonds: 66
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C31 C32 C C doub 1.36 N Y
2 C31 C30 C C sing 1.39 N Y
3 C32 C27 C C sing 1.41 N Y
4 C30 C29 C C doub 1.36 N Y
5 C26 C27 C C doub 1.41 N Y
6 C26 C25 C C sing 1.36 N Y
7 C27 C28 C C sing 1.42 N Y
8 C29 C28 C C sing 1.41 N Y
9 C25 C24 C C doub 1.39 N Y
10 C28 C23 C C doub 1.4 N Y
11 C24 C23 C C sing 1.36 N Y
12 C23 C02 C C sing 1.51 N N
13 C02 C01 C C sing 1.53 N N
14 C02 N03 C N sing 1.47 N N
15 N03 C22 N C sing 1.47 N N
16 N03 C04 N C sing 1.47 N N
17 C22 C21 C C sing 1.53 N N
18 C04 C05 C C sing 1.53 N N
19 C21 C06 C C sing 1.53 N N
20 C05 C06 C C sing 1.53 N N
21 C06 C07 C C sing 1.51 N N
22 N08 C07 N C sing 1.35 N N
23 N08 C09 N C sing 1.46 N N
24 C07 O20 C O doub 1.21 N N
25 C09 C10 C C sing 1.51 N N
26 C10 C11 C C doub 1.38 N Y
27 C10 C19 C C sing 1.38 N Y
28 C11 C12 C C sing 1.38 N Y
29 C19 C14 C C doub 1.39 N Y
30 C12 C13 C C doub 1.38 N Y
31 O18 C16 O C doub 1.21 N N
32 C14 C13 C C sing 1.39 N Y
33 C14 N15 C N sing 1.4 N N
34 C16 N15 C N sing 1.35 N N
35 C16 C17 C C sing 1.51 N N
36 C19 H1 C H sing 1.08 N N
37 C21 H2 C H sing 1.09 N N
38 C21 H3 C H sing 1.09 N N
39 C22 H4 C H sing 1.09 N N
40 C22 H5 C H sing 1.09 N N
41 C24 H6 C H sing 1.08 N N
42 C25 H7 C H sing 1.08 N N
43 C26 H8 C H sing 1.08 N N
44 C11 H9 C H sing 1.08 N N
45 C12 H10 C H sing 1.08 N N
46 C13 H11 C H sing 1.08 N N
47 C17 H12 C H sing 1.09 N N
48 C17 H13 C H sing 1.09 N N
49 C17 H14 C H sing 1.09 N N
50 C01 H15 C H sing 1.09 N N
51 C01 H16 C H sing 1.09 N N
52 C01 H17 C H sing 1.09 N N
53 C02 H18 C H sing 1.09 N N
54 C04 H19 C H sing 1.09 N N
55 C04 H20 C H sing 1.09 N N
56 C05 H21 C H sing 1.09 N N
57 C05 H22 C H sing 1.09 N N
58 C06 H23 C H sing 1.09 N N
59 C09 H24 C H sing 1.09 N N
60 C09 H25 C H sing 1.09 N N
61 C29 H26 C H sing 1.08 N N
62 C30 H27 C H sing 1.08 N N
63 C31 H28 C H sing 1.08 N N
64 C32 H29 C H sing 1.08 N N
65 N08 H31 N H sing 0.97 N N
66 N15 H32 N H sing 0.97 N N



GYX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GYX 7e35 Open in New Window Bound ligand 2 1