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532 : Summary

Code

532

One-letter code

X

Molecule name

(5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one
OpenEye OEToolkits 1.7.2 (5S)-2-azanyl-3-methyl-5-(3-pyridin-3-ylphenyl)-5-thiophen-3-yl-imidazol-4-one

Formula

C19 H16 N4 O S

Formal charge

0

Molecular weight

348.422 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C4N(C(=NC4(c1ccsc1)c3cccc(c2cccnc2)c3)N)C
SMILES CACTVS 3.370 CN1C(=N[C](C1=O)(c2cscc2)c3cccc(c3)c4cccnc4)N
SMILES OpenEye OEToolkits 1.7.2 CN1C(=O)C(N=C1N)(c2cccc(c2)c3cccnc3)c4ccsc4
Canonical SMILES CACTVS 3.370 CN1C(=N[C@](C1=O)(c2cscc2)c3cccc(c3)c4cccnc4)N
Canonical SMILES OpenEye OEToolkits 1.7.2 CN1C(=O)[C@](N=C1N)(c2cccc(c2)c3cccnc3)c4ccsc4

IUPAC InChI

InChI=1S/C19H16N4OS/c1-23-17(24)19(22-18(23)20,16-7-9-25-12-16)15-6-2-4-13(10-15)14-5-3-8-21-11-14/h2-12H,1H3,(H2,20,22)/t19-/m0/s1

IUPAC InChI key

AOGBXAFIKRFUPJ-IBGZPJMESA-N
532

wwPDB Information

Atom count

41 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-06-03

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



532 : 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 C1 C C1 N N N 0 2.825 3.533 1.126
2 N1 N N1 N N N 0 2.157 2.386 0.506
3 O1 O O1 N N N 0 2.611 0.768 2.074
4 S1 S S1 N Y N 0 3.746 -2.78 -0.73
5 C2 C C2 N N N 0 2.118 1.143 1.031
6 N2 N N2 N N N 0 0.982 1.278 -1.024
7 C3 C C3 S N N 0 1.326 0.318 0.037
8 N3 N N3 N N N 0 1.349 3.566 -1.448
9 C4 C C4 N N N 0 1.48 2.428 -0.688
10 N4 N N4 N Y N 0 -4.911 0.635 -1.688
11 C5 C C5 N Y N 0 0.077 -0.229 0.68
12 C6 C C6 N Y N 0 0.166 -0.946 1.859
13 C7 C C7 N Y N 0 -0.976 -1.452 2.454
14 C8 C C8 N Y N 0 -2.211 -1.242 1.875
15 C9 C C9 N Y N 0 -2.306 -0.519 0.687
16 C10 C C10 N Y N 0 -1.153 -0.008 0.094
17 C11 C C11 N Y N 0 -3.63 -0.291 0.058
18 C12 C C12 N Y N 0 -4.793 -0.795 0.648
19 C13 C C13 N Y N 0 -6.004 -0.555 0.022
20 C14 C C14 N Y N 0 -6.025 0.171 -1.155
21 C15 C C15 N Y N 0 -3.735 0.431 -1.129
22 C16 C C16 N Y N 0 2.171 -0.8 -0.516
23 C17 C C17 N Y N 0 2.254 -1.071 -1.87
24 C18 C C18 N Y N 0 3.047 -2.095 -2.191
25 C19 C C19 N Y N 0 2.897 -1.603 0.264
26 H1 H H1 N N N 0 3.859 3.58 0.784
27 H1A H H1A N N N 0 2.307 4.45 0.846
28 H1B H H1B N N N 0 2.805 3.421 2.211
29 HN3 H HN3 N N N 0 1.746 4.398 -1.148
30 HN3A H HN3A N N N 0 0.858 3.536 -2.284
31 H6 H H6 N N N 0 1.13 -1.113 2.316
32 H7 H H7 N N N 0 -0.901 -2.012 3.375
33 H8 H H8 N N N 0 -3.101 -1.637 2.34
34 H10 H H10 N N N 0 -1.222 0.557 -0.824
35 H12 H H12 N N N 0 -4.747 -1.359 1.568
36 H17 H H17 N N N 0 1.717 -0.498 -2.612
37 H13 H H13 N N N 0 -6.922 -0.93 0.449
38 H14 H H14 N N N 0 -6.968 0.361 -1.645
39 H15 H H15 N N N 0 -2.845 0.827 -1.595
40 H18 H H18 N N N 0 3.231 -2.448 -3.195
41 H19 H H19 N N N 0 2.954 -1.541 1.34



532 : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N1 C N sing 1.47 N N
2 N1 C2 N C sing 1.35 N N
3 N1 C4 N C sing 1.37 N N
4 O1 C2 O C doub 1.21 N N
5 S1 C18 S C sing 1.76 N Y
6 S1 C19 S C sing 1.76 N Y
7 C2 C3 C C sing 1.52 N N
8 N2 C3 N C sing 1.47 N N
9 N2 C4 N C doub 1.3 N N
10 C3 C5 C C sing 1.51 N N
11 C3 C16 C C sing 1.51 N N
12 N3 C4 N C sing 1.37 N N
13 N4 C14 N C doub 1.32 N Y
14 N4 C15 N C sing 1.32 N Y
15 C5 C6 C C doub 1.38 N Y
16 C5 C10 C C sing 1.38 N Y
17 C6 C7 C C sing 1.38 N Y
18 C7 C8 C C doub 1.38 N Y
19 C8 C9 C C sing 1.39 N Y
20 C9 C10 C C doub 1.39 N Y
21 C9 C11 C C sing 1.48 N Y
22 C11 C12 C C sing 1.4 N Y
23 C11 C15 C C doub 1.39 N Y
24 C12 C13 C C doub 1.38 N Y
25 C13 C14 C C sing 1.38 N Y
26 C16 C17 C C sing 1.38 N Y
27 C16 C19 C C doub 1.33 N Y
28 C17 C18 C C doub 1.33 N Y
29 C1 H1 C H sing 1.09 N N
30 C1 H1A C H sing 1.09 N N
31 C1 H1B C H sing 1.09 N N
32 N3 HN3 N H sing 0.97 N N
33 N3 HN3A N H sing 0.97 N N
34 C6 H6 C H sing 1.08 N N
35 C7 H7 C H sing 1.08 N N
36 C8 H8 C H sing 1.08 N N
37 C10 H10 C H sing 1.08 N N
38 C12 H12 C H sing 1.08 N N
39 C13 H13 C H sing 1.08 N N
40 C14 H14 C H sing 1.08 N N
41 C15 H15 C H sing 1.08 N N
42 C17 H17 C H sing 1.08 N N
43 C18 H18 C H sing 1.08 N N
44 C19 H19 C H sing 1.08 N N



532 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
532 3s7m Open in New Window Bound ligand 1 1