Chemical Components in the PDB

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A1AK3 : Summary

Code

A1AK3

One-letter code

X

Molecule name

4-{[(1S)-1-(1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~-benzothiopyran-7-yl)-2-methylpropyl]amino}-N-[(3R)-1-methylpyrrolidin-3-yl]-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 4-{[(1S)-1-(1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~-benzothiopyran-7-yl)-2-methylpropyl]amino}-N-[(3R)-1-methylpyrrolidin-3-yl]-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide
OpenEye OEToolkits 2.0.7 4-[[(1~{S})-1-[1,1-bis(oxidanylidene)-3,4-dihydro-2~{H}-thiochromen-7-yl]-2-methyl-propyl]amino]-~{N}-[(3~{S})-1-methylpyrrolidin-3-yl]-7~{H}-pyrrolo[2,3-d]pyrimidine-6-carboxamide

Formula

C25 H32 N6 O3 S

Formal charge

0

Molecular weight

496.625 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CN1CCC(C1)NC(=O)c1cc2c([NH]1)ncnc2NC(c1ccc2CCCS(=O)(=O)c2c1)C(C)C
SMILES CACTVS 3.385 CC(C)[CH](Nc1ncnc2[nH]c(cc12)C(=O)N[CH]3CCN(C)C3)c4ccc5CCC[S](=O)(=O)c5c4
SMILES OpenEye OEToolkits 2.0.7 CC(C)C(c1ccc2c(c1)S(=O)(=O)CCC2)Nc3c4cc([nH]c4ncn3)C(=O)NC5CCN(C5)C
Canonical SMILES CACTVS 3.385 CC(C)[C@H](Nc1ncnc2[nH]c(cc12)C(=O)N[C@H]3CCN(C)C3)c4ccc5CCC[S](=O)(=O)c5c4
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(C)[C@@H](c1ccc2c(c1)S(=O)(=O)CCC2)Nc3c4cc([nH]c4ncn3)C(=O)N[C@H]5CCN(C5)C

IUPAC InChI

InChI=1S/C25H32N6O3S/c1-15(2)22(17-7-6-16-5-4-10-35(33,34)21(16)11-17)30-24-19-12-20(29-23(19)26-14-27-24)25(32)28-18-8-9-31(3)13-18/h6-7,11-12,14-15,18,22H,4-5,8-10,13H2,1-3H3,(H,28,32)(H2,26,27,29,30)/t18-,22+/m1/s1

IUPAC InChI key

QEVYAPKJBMOYGR-GCJKJVERSA-N
A1AK3

wwPDB Information

Atom count

67 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2024-04-05

Last modified at

2024-05-10

Status

Released

Obsoleted

Not Assigned



A1AK3 : Atoms of Molecule

Total Number of Atoms: 67
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -0.14 -3.01 -0.8
2 N3 N N2 N N N 0 5.945 0.017 0.071
3 C4 C C1 N Y N 0 -3.047 -0.294 0.558
4 C5 C C2 N Y N 0 -4.204 -0.174 -0.183
5 C6 C C3 N Y N 0 -5.022 0.938 -0.043
6 C7 C C4 N N N 0 -7.423 2.39 -0.305
7 C8 C C5 N N N 0 -6.434 3.536 -0.044
8 C10 C C6 N Y N 0 -4.691 1.934 0.846
9 C13 C C7 N Y N 0 0.196 -1.883 -0.18
10 C15 C C8 N Y N 0 2.489 -2.345 -0.807
11 C17 C C9 N Y N 0 2.272 -0.419 0.374
12 C20 C C10 S N N 0 7.038 0.919 0.442
13 C21 C C11 N N N 0 7.199 2.041 -0.606
14 C22 C C12 N N N 0 8.995 3.669 -0.518
15 C24 C C13 N N N 0 8.402 0.183 0.378
16 O2 O O1 N N N 0 4.446 1.314 1.075
17 C19 C C14 N N N 0 4.68 0.305 0.437
18 C23 C C15 N N N 0 9.38 1.357 0.119
19 N4 N N3 N N N 0 8.645 2.268 -0.785
20 C18 C C16 N Y N 0 3.585 -0.599 0.065
21 N5 N N4 N Y N 0 3.72 -1.773 -0.655
22 N2 N N5 N Y N 0 2.05 -3.453 -1.4
23 C14 C C17 N Y N 0 0.772 -3.763 -1.388
24 C16 C C18 N Y N 0 1.554 -1.507 -0.164
25 N N N6 N N N 0 -0.762 -1.101 0.433
26 C3 C C19 S N N 0 -2.168 -1.509 0.405
27 C1 C C20 N N N 0 -2.44 -2.482 1.553
28 C2 C C21 N N N 0 -3.909 -2.908 1.524
29 C C C22 N N N 0 -1.548 -3.716 1.398
30 C12 C C23 N Y N 0 -2.697 0.714 1.438
31 C11 C C24 N Y N 0 -3.513 1.814 1.582
32 S S S1 N N N 0 -6.475 1.026 -1.043
33 O O O2 N N N 0 -5.996 1.389 -2.331
34 O1 O O3 N N N 0 -7.13 -0.216 -0.824
35 C9 C C25 N N N 0 -5.524 3.154 1.109
36 H22 H H1 N N N 0 6.131 -0.788 -0.438
37 H10 H H2 N N N 0 -4.476 -0.954 -0.879
38 H12 H H3 N N N 0 -7.871 2.065 0.634
39 H11 H H4 N N N 0 -8.201 2.719 -0.994
40 H13 H H5 N N N 0 -5.836 3.712 -0.938
41 H14 H H6 N N N 0 -6.985 4.442 0.211
42 H21 H H7 N N N 0 1.855 0.408 0.931
43 H1 H H8 N N N 0 6.87 1.339 1.433
44 H24 H H9 N N N 0 6.752 1.732 -1.551
45 H23 H H10 N N N 0 6.722 2.953 -0.248
46 H25 H H11 N N N 0 8.726 3.922 0.507
47 H26 H H12 N N N 0 10.067 3.809 -0.657
48 H27 H H13 N N N 0 8.452 4.317 -1.207
49 H31 H H14 N N N 0 8.625 -0.309 1.324
50 H30 H H15 N N N 0 8.423 -0.531 -0.445
51 H29 H H16 N N N 0 9.62 1.863 1.054
52 H28 H H17 N N N 0 10.289 0.995 -0.361
53 H2 H H19 N N N 0 4.554 -2.132 -0.997
54 H20 H H20 N N N 0 0.454 -4.67 -1.88
55 H19 H H21 N N N 0 -0.503 -0.281 0.882
56 H H H22 N N N 0 -2.386 -1.997 -0.545
57 H6 H H23 N N N 0 -2.222 -1.994 2.503
58 H7 H H24 N N N 0 -4.127 -3.397 0.575
59 H9 H H25 N N N 0 -4.102 -3.602 2.342
60 H8 H H26 N N N 0 -4.544 -2.03 1.635
61 H3 H H27 N N N 0 -0.501 -3.412 1.418
62 H4 H H28 N N N 0 -1.741 -4.41 2.216
63 H5 H H29 N N N 0 -1.766 -4.204 0.448
64 H18 H H30 N N N 0 -1.787 0.636 2.015
65 H17 H H31 N N N 0 -3.234 2.596 2.273
66 H15 H H32 N N N 0 -4.858 3.991 1.319
67 H16 H H33 N N N 0 -6.137 2.972 1.992



A1AK3 : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C C1 C C sing 1.53 N N
2 C2 C1 C C sing 1.53 N N
3 C1 C3 C C sing 1.53 N N
4 C4 C3 C C sing 1.51 N N
5 C4 C5 C C doub 1.38 N Y
6 C5 C6 C C sing 1.39 N Y
7 C6 S C S sing 1.77 N N
8 S C7 S C sing 1.82 N N
9 C7 C8 C C sing 1.54 N N
10 C8 C9 C C sing 1.52 N N
11 O S O S doub 1.42 N N
12 O1 S O S doub 1.42 N N
13 C6 C10 C C doub 1.38 N Y
14 C9 C10 C C sing 1.5 N N
15 C10 C11 C C sing 1.39 N Y
16 C11 C12 C C doub 1.38 N Y
17 C12 C4 C C sing 1.38 N Y
18 C3 N C N sing 1.46 N N
19 N C13 N C sing 1.38 N N
20 C13 N1 C N doub 1.33 N Y
21 N1 C14 N C sing 1.32 N Y
22 C14 N2 C N doub 1.32 N Y
23 N2 C15 N C sing 1.33 N Y
24 C15 C16 C C doub 1.41 N Y
25 C13 C16 C C sing 1.41 N Y
26 C16 C17 C C sing 1.41 N Y
27 C17 C18 C C doub 1.36 N Y
28 C18 C19 C C sing 1.47 N N
29 N3 C19 N C sing 1.35 N N
30 C20 N3 C N sing 1.46 N N
31 C20 C21 C C sing 1.54 N N
32 C21 N4 C N sing 1.47 N N
33 C22 N4 C N sing 1.47 N N
34 N4 C23 N C sing 1.48 N N
35 C23 C24 C C sing 1.55 N N
36 C24 C20 C C sing 1.55 N N
37 C19 O2 C O doub 1.22 N N
38 N5 C18 N C sing 1.38 N Y
39 C15 N5 C N sing 1.37 N Y
40 N3 H22 N H sing 0.97 N N
41 C5 H10 C H sing 1.08 N N
42 C7 H12 C H sing 1.09 N N
43 C7 H11 C H sing 1.09 N N
44 C8 H13 C H sing 1.09 N N
45 C8 H14 C H sing 1.09 N N
46 C17 H21 C H sing 1.08 N N
47 C20 H1 C H sing 1.09 N N
48 C21 H24 C H sing 1.09 N N
49 C21 H23 C H sing 1.09 N N
50 C22 H25 C H sing 1.09 N N
51 C22 H26 C H sing 1.09 N N
52 C22 H27 C H sing 1.09 N N
53 C24 H31 C H sing 1.09 N N
54 C24 H30 C H sing 1.09 N N
55 C23 H29 C H sing 1.09 N N
56 C23 H28 C H sing 1.09 N N
57 N5 H2 N H sing 0.97 N N
58 C14 H20 C H sing 1.08 N N
59 N H19 N H sing 0.97 N N
60 C3 H C H sing 1.09 N N
61 C1 H6 C H sing 1.09 N N
62 C2 H7 C H sing 1.09 N N
63 C2 H9 C H sing 1.09 N N
64 C2 H8 C H sing 1.09 N N
65 C H3 C H sing 1.09 N N
66 C H4 C H sing 1.09 N N
67 C H5 C H sing 1.09 N N
68 C12 H18 C H sing 1.08 N N
69 C11 H17 C H sing 1.08 N N
70 C9 H15 C H sing 1.09 N N
71 C9 H16 C H sing 1.09 N N



A1AK3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
A1AK3 7gzv Open in New Window Bound ligand 1 1