Chemical Components in the PDB

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LR4 : Summary

Code

LR4

One-letter code

X

Molecule name

(4~{S})-2-azanyl-4-[3-[6-[(2~{S})-2,4-dimethylpiperazin-1-yl]pyridin-2-yl]-1,2,4-oxadiazol-5-yl]-4-methyl-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile

Systematic names

ProgramVersionName
OpenEye OEToolkits 3.1.0.0 (4~{S})-2-azanyl-4-[3-[6-[(2~{S})-2,4-dimethylpiperazin-1-yl]pyridin-2-yl]-1,2,4-oxadiazol-5-yl]-4-methyl-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile

Formula

C23 H27 N7 O S

Formal charge

0

Molecular weight

449.572 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH]1CN(C)CCN1c2cccc(n2)c3noc(n3)[C]4(C)CCCc5sc(N)c(C#N)c45
SMILES OpenEye OEToolkits 3.1.0.0 CC1CN(CCN1c2cccc(n2)c3nc(on3)C4(CCCc5c4c(c(s5)N)C#N)C)C
Canonical SMILES CACTVS 3.385 C[C@H]1CN(C)CCN1c2cccc(n2)c3noc(n3)[C@@]4(C)CCCc5sc(N)c(C#N)c45
Canonical SMILES OpenEye OEToolkits 3.1.0.0 C[C@H]1CN(CCN1c2cccc(n2)c3nc(on3)[C@]4(CCCc5c4c(c(s5)N)C#N)C)C

IUPAC InChI

InChI=1S/C23H27N7OS/c1-14-13-29(3)10-11-30(14)18-8-4-6-16(26-18)21-27-22(31-28-21)23(2)9-5-7-17-19(23)15(12-24)20(25)32-17/h4,6,8,14H,5,7,9-11,13,25H2,1-3H3/t14-,23-/m0/s1

IUPAC InChI key

YZNVUBRDUJUVPB-PSLXWICFSA-N
LR4

wwPDB Information

Atom count

59 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-07-11

Last modified at

2023-06-02

Status

Released

Obsoleted

Not Assigned



LR4 : Atoms of Molecule

Total Number of Atoms: 59
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 S N N 0 -3.338 -1.285 -0.77
2 C5 C C2 N Y N 0 -5.089 0.012 0.495
3 C6 C C3 N Y N 0 -3.989 -0.006 -0.266
4 C7 C C4 N Y N 0 -3.492 1.328 -0.554
5 C8 C C5 N Y N 0 -4.247 2.319 0.008
6 C10 C C6 N N N 0 -3.696 -1.498 -2.242
7 C17 C C7 N Y N 0 1.276 -0.664 1.029
8 C20 C C8 N Y N 0 3.408 -0.191 2.665
9 C21 C C9 N Y N 0 2.142 -0.231 3.221
10 C22 C C10 N Y N 0 1.059 -0.472 2.389
11 C26 C C11 S N N 0 4.76 -0.564 -0.725
12 C1 C C12 N N N 0 -5.83 -1.228 0.957
13 C11 C C13 N Y N 0 -1.841 -1.184 -0.623
14 C14 C C14 N Y N 0 0.124 -0.923 0.13
15 C19 C C15 N Y N 0 3.556 -0.381 1.293
16 C2 C C16 N N N 0 -5.387 -2.415 0.097
17 C23 C C17 N N N 0 -2.327 1.58 -1.348
18 C27 C C18 N N N 0 6.179 -0.593 -1.298
19 C29 C C19 N N N 0 6.918 0.899 0.459
20 C3 C C20 N N N 0 -3.856 -2.461 0.06
21 C30 C C21 N N N 0 5.499 0.928 1.032
22 C31 C C22 N N N 0 8.194 0.718 -1.591
23 C32 C C23 N N N 0 3.967 0.569 -1.38
24 N13 N N1 N Y N 0 0.183 -1.218 -1.143
25 N15 N N2 N Y N 0 -1.184 -0.902 0.474
26 N16 N N3 N N N 0 -3.987 3.673 -0.117
27 N18 N N4 N Y N 0 2.504 -0.614 0.526
28 N24 N N5 N N N 0 -1.403 1.779 -1.977
29 N25 N N6 N N N 0 4.824 -0.342 0.726
30 N28 N N7 N N N 0 6.853 0.677 -0.992
31 O12 O O1 N Y N 0 -0.934 -1.372 -1.588
32 S9 S S1 N Y N 0 -5.551 1.661 0.882
33 H1 H H1 N N N 0 -4.779 -1.565 -2.346
34 H2 H H2 N N N 0 -3.326 -0.659 -2.831
35 H3 H H3 N N N 0 -3.238 -2.421 -2.597
36 H4 H H4 N N N 0 4.272 -0.013 3.287
37 H5 H H5 N N N 0 2.001 -0.087 4.282
38 H6 H H6 N N N 0 0.057 -0.509 2.793
39 H7 H H7 N N N 0 4.267 -1.516 -0.925
40 H8 H H8 N N N 0 -5.594 -1.426 2.003
41 H9 H H9 N N N 0 -6.903 -1.075 0.844
42 H10 H H10 N N N 0 -5.769 -3.34 0.528
43 H11 H H11 N N N 0 -5.772 -2.296 -0.915
44 H12 H H12 N N N 0 6.735 -1.417 -0.85
45 H13 H H13 N N N 0 6.132 -0.729 -2.378
46 H14 H H14 N N N 0 7.41 1.851 0.66
47 H15 H H15 N N N 0 7.482 0.092 0.927
48 H16 H H16 N N N 0 -3.531 -3.398 -0.393
49 H17 H H17 N N N 0 -3.465 -2.391 1.075
50 H18 H H18 N N N 0 5.545 1.064 2.112
51 H19 H H19 N N N 0 4.943 1.752 0.585
52 H20 H H20 N N N 0 8.111 0.618 -2.673
53 H21 H H21 N N N 0 8.671 1.668 -1.349
54 H22 H H22 N N N 0 8.794 -0.101 -1.195
55 H23 H H23 N N N 0 4.461 1.52 -1.181
56 H24 H H24 N N N 0 3.92 0.403 -2.457
57 H25 H H25 N N N 0 2.957 0.59 -0.971
58 H26 H H26 N N N 0 -3.223 3.974 -0.633
59 H27 H H27 N N N 0 -4.568 4.32 0.312



LR4 : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C31 N28 C N sing 1.47 N N
2 N16 C8 N C sing 1.38 N N
3 C27 N28 C N sing 1.47 N N
4 C27 C26 C C sing 1.53 N N
5 S9 C8 S C sing 1.7 N Y
6 S9 C5 S C sing 1.76 N Y
7 N28 C29 N C sing 1.47 N N
8 C8 C7 C C doub 1.37 N Y
9 C29 C30 C C sing 1.53 N N
10 C26 C32 C C sing 1.53 N N
11 C26 N25 C N sing 1.47 N N
12 C7 C23 C C sing 1.43 N N
13 C7 C6 C C sing 1.45 N Y
14 C5 C1 C C sing 1.52 N N
15 C5 C6 C C doub 1.34 N Y
16 N13 O12 N O sing 1.21 N Y
17 N13 C14 N C doub 1.31 N Y
18 O12 C11 O C sing 1.34 N Y
19 C23 N24 C N trip 1.14 N N
20 C1 C2 C C sing 1.53 N N
21 C6 C4 C C sing 1.52 N N
22 N25 C30 N C sing 1.47 N N
23 N25 C19 N C sing 1.39 N N
24 N18 C19 N C doub 1.32 N Y
25 N18 C17 N C sing 1.33 N Y
26 C14 C17 C C sing 1.48 N N
27 C14 N15 C N sing 1.35 N Y
28 C11 C4 C C sing 1.51 N N
29 C11 N15 C N doub 1.31 N Y
30 C19 C20 C C sing 1.39 N Y
31 C17 C22 C C doub 1.39 N Y
32 C4 C3 C C sing 1.53 N N
33 C4 C10 C C sing 1.53 N N
34 C2 C3 C C sing 1.53 N N
35 C20 C21 C C doub 1.38 N Y
36 C22 C21 C C sing 1.39 N Y
37 C10 H1 C H sing 1.09 N N
38 C10 H2 C H sing 1.09 N N
39 C10 H3 C H sing 1.09 N N
40 C20 H4 C H sing 1.08 N N
41 C21 H5 C H sing 1.08 N N
42 C22 H6 C H sing 1.08 N N
43 C26 H7 C H sing 1.09 N N
44 C1 H8 C H sing 1.09 N N
45 C1 H9 C H sing 1.09 N N
46 C2 H10 C H sing 1.09 N N
47 C2 H11 C H sing 1.09 N N
48 C27 H12 C H sing 1.09 N N
49 C27 H13 C H sing 1.09 N N
50 C29 H14 C H sing 1.09 N N
51 C29 H15 C H sing 1.09 N N
52 C3 H16 C H sing 1.09 N N
53 C3 H17 C H sing 1.09 N N
54 C30 H18 C H sing 1.09 N N
55 C30 H19 C H sing 1.09 N N
56 C31 H20 C H sing 1.09 N N
57 C31 H21 C H sing 1.09 N N
58 C31 H22 C H sing 1.09 N N
59 C32 H23 C H sing 1.09 N N
60 C32 H24 C H sing 1.09 N N
61 C32 H25 C H sing 1.09 N N
62 N16 H26 N H sing 0.97 N N
63 N16 H27 N H sing 0.97 N N



LR4 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LR4 8azr Open in New Window Bound ligand 1 1