Chemical Components in the PDB

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Y44 : Summary

Code

Y44

One-letter code

X

Molecule name

N-[(pyridin-3-yl)methyl]-4-(thiophene-2-carbonyl)piperazine-1-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(pyridin-3-yl)methyl]-4-(thiophene-2-carbonyl)piperazine-1-carboxamide
OpenEye OEToolkits 2.0.7 ~{N}-(pyridin-3-ylmethyl)-4-thiophen-2-ylcarbonyl-piperazine-1-carboxamide

Formula

C16 H18 N4 O2 S

Formal charge

0

Molecular weight

330.405 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N(Cc1cccnc1)C(N3CCN(C(=O)c2cccs2)CC3)=O
SMILES CACTVS 3.385 O=C(NCc1cccnc1)N2CCN(CC2)C(=O)c3sccc3
SMILES OpenEye OEToolkits 2.0.7 c1cc(cnc1)CNC(=O)N2CCN(CC2)C(=O)c3cccs3
Canonical SMILES CACTVS 3.385 O=C(NCc1cccnc1)N2CCN(CC2)C(=O)c3sccc3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(cnc1)CNC(=O)N2CCN(CC2)C(=O)c3cccs3

IUPAC InChI

InChI=1S/C16H18N4O2S/c21-15(14-4-2-10-23-14)19-6-8-20(9-7-19)16(22)18-12-13-3-1-5-17-11-13/h1-5,10-11H,6-9,12H2,(H,18,22)

IUPAC InChI key

QWTHOPVYVVYMKH-UHFFFAOYSA-N
Y44

wwPDB Information

Atom count

41 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-02-03

Last modified at

2021-02-12

Status

Released

Obsoleted

Not Assigned



Y44 : 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 N1 N N1 N N N 0 -2.442 -0.899 0.094
2 N3 N N2 N N N 0 -0.259 -1.691 0.332
3 C4 C C1 N Y N 0 -4.792 0.948 -1.201
4 C5 C C2 N Y N 0 -5.504 2.13 -1.065
5 C6 C C3 N Y N 0 -6.016 2.469 0.173
6 C7 C C4 N Y N 0 -5.17 0.548 1.122
7 C8 C C5 N N N 0 0.715 -2.792 0.296
8 C10 C C6 N N N 0 3.618 -0.835 -0.065
9 C13 C C7 N Y N 0 5.428 2.275 0.773
10 C15 C C8 N N N 0 1.343 0.038 -0.298
11 C1 C C9 N N N 0 -1.561 -1.919 0.069
12 C11 C C10 N Y N 0 4.108 0.539 0.075
13 C12 C C11 N Y N 0 5.19 0.922 0.818
14 C14 C C12 N Y N 0 4.573 2.977 0.021
15 C16 C C13 N N N 0 0.212 -0.34 0.667
16 C2 C C14 N N N 0 -3.859 -1.149 -0.18
17 C3 C C15 N Y N 0 -4.625 0.146 -0.083
18 C9 C C16 N N N 0 1.846 -2.414 -0.668
19 N2 N N3 N Y N 0 -5.832 1.684 1.217
20 N4 N N4 N N N 0 2.316 -1.062 -0.334
21 O1 O O1 N N N 0 -1.941 -3.044 -0.192
22 O2 O O2 N N N 0 4.385 -1.772 0.06
23 S1 S S1 N Y N 0 3.405 1.957 -0.69
24 H1 H H1 N N N 0 -2.138 -0.001 0.298
25 H4 H H2 N N N 0 -4.381 0.657 -2.157
26 H5 H H3 N N N 0 -5.657 2.777 -1.916
27 H6 H H4 N N N 0 -6.571 3.388 0.287
28 H7 H H5 N N N 0 -5.044 -0.071 1.998
29 H9 H H6 N N N 0 1.123 -2.951 1.294
30 H8 H H7 N N N 0 0.226 -3.701 -0.052
31 H13 H H8 N N N 0 6.243 2.738 1.309
32 H16 H H9 N N N 0 0.934 0.198 -1.296
33 H15 H H10 N N N 0 1.829 0.95 0.049
34 H12 H H11 N N N 0 5.797 0.231 1.383
35 H14 H H12 N N N 0 4.616 4.048 -0.118
36 H18 H H13 N N N 0 -0.61 0.369 0.563
37 H17 H H14 N N N 0 0.584 -0.325 1.691
38 H2 H H15 N N N 0 -3.968 -1.561 -1.183
39 H3 H H16 N N N 0 -4.251 -1.858 0.549
40 H11 H H17 N N N 0 2.667 -3.123 -0.565
41 H10 H H18 N N N 0 1.474 -2.428 -1.693



Y44 : 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 O1 C1 O C doub 1.22 N N
2 C1 N1 C N sing 1.35 N N
3 N1 C2 N C sing 1.46 N N
4 C2 C3 C C sing 1.51 N N
5 C3 C4 C C doub 1.39 N Y
6 C4 C5 C C sing 1.39 N Y
7 C5 C6 C C doub 1.38 N Y
8 C6 N2 C N sing 1.32 N Y
9 N2 C7 N C doub 1.32 N Y
10 C1 N3 C N sing 1.35 N N
11 N3 C8 N C sing 1.47 N N
12 C8 C9 C C sing 1.53 N N
13 C9 N4 C N sing 1.47 N N
14 N4 C10 N C sing 1.35 N N
15 C10 O2 C O doub 1.22 N N
16 C10 C11 C C sing 1.47 N N
17 C11 C12 C C doub 1.37 N Y
18 C12 C13 C C sing 1.37 N Y
19 C13 C14 C C doub 1.34 N Y
20 C14 S1 C S sing 1.71 N Y
21 N4 C15 N C sing 1.47 N N
22 C15 C16 C C sing 1.53 N N
23 C3 C7 C C sing 1.38 N Y
24 N3 C16 N C sing 1.47 N N
25 C11 S1 C S sing 1.76 N Y
26 N1 H1 N H sing 0.97 N N
27 C4 H4 C H sing 1.08 N N
28 C5 H5 C H sing 1.08 N N
29 C6 H6 C H sing 1.08 N N
30 C7 H7 C H sing 1.08 N N
31 C8 H9 C H sing 1.09 N N
32 C8 H8 C H sing 1.09 N N
33 C13 H13 C H sing 1.08 N N
34 C15 H16 C H sing 1.09 N N
35 C15 H15 C H sing 1.09 N N
36 C12 H12 C H sing 1.08 N N
37 C14 H14 C H sing 1.08 N N
38 C16 H18 C H sing 1.09 N N
39 C16 H17 C H sing 1.09 N N
40 C2 H2 C H sing 1.09 N N
41 C2 H3 C H sing 1.09 N N
42 C9 H11 C H sing 1.09 N N
43 C9 H10 C H sing 1.09 N N



Y44 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Y44 5s9d Open in New Window Bound ligand 1 1