Chemical Components in the PDB

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9GS : Summary

Code

9GS

One-letter code

X

Molecule name

5'-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-N-{[4-(ethylsulfonyl)phenyl]methyl}spiro[cyclopentane-1,3'-pyrrolo[3,2-b]pyridine]-1'(2'H)-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-N-{[4-(ethylsulfonyl)phenyl]methyl}spiro[cyclopentane-1,3'-pyrrolo[3,2-b]pyridine]-1'(2'H)-carboxamide
OpenEye OEToolkits 2.0.6 5-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-~{N}-[(4-ethylsulfonylphenyl)methyl]spiro[2~{H}-pyrrolo[3,2-b]pyridine-3,1'-cyclopentane]-1-carboxamide

Formula

C29 H33 N5 O4 S

Formal charge

0

Molecular weight

547.668 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c1(ccc(cc1)CNC(=O)N4CC2(CCCC2)c3nc(ccc34)c5c(OC)ncnc5C6CC6)S(CC)(=O)=O
SMILES CACTVS 3.385 CC[S](=O)(=O)c1ccc(CNC(=O)N2CC3(CCCC3)c4nc(ccc24)c5c(OC)ncnc5C6CC6)cc1
SMILES OpenEye OEToolkits 2.0.6 CCS(=O)(=O)c1ccc(cc1)CNC(=O)N2CC3(CCCC3)c4c2ccc(n4)c5c(ncnc5OC)C6CC6
Canonical SMILES CACTVS 3.385 CC[S](=O)(=O)c1ccc(CNC(=O)N2CC3(CCCC3)c4nc(ccc24)c5c(OC)ncnc5C6CC6)cc1
Canonical SMILES OpenEye OEToolkits 2.0.6 CCS(=O)(=O)c1ccc(cc1)CNC(=O)N2CC3(CCCC3)c4c2ccc(n4)c5c(ncnc5OC)C6CC6

IUPAC InChI

InChI=1S/C29H33N5O4S/c1-3-39(36,37)21-10-6-19(7-11-21)16-30-28(35)34-17-29(14-4-5-15-29)26-23(34)13-12-22(33-26)24-25(20-8-9-20)31-18-32-27(24)38-2/h6-7,10-13,18,20H,3-5,8-9,14-17H2,1-2H3,(H,30,35)

IUPAC InChI key

PWIXSNKHPMGRRW-UHFFFAOYSA-N
9GS

wwPDB Information

Atom count

72 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-05-10

Last modified at

2018-05-11

Status

Released

Obsoleted

Not Assigned



9GS : Atoms of Molecule

Total Number of Atoms: 72
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C6 C C1 N Y N 0 6.874 0.57 0.248
2 C7 C C2 N Y N 0 6.299 1.241 -0.815
3 C8 C C3 N Y N 0 5.027 1.767 -0.694
4 C10 C C4 N N N 0 2.942 2.196 0.622
5 C15 C C5 N N N 0 0.048 -0.82 -0.515
6 C17 C C6 N N N 0 -1.513 -1.986 -2.13
7 C20 C C7 N N N 0 -1.424 -2.754 0.188
8 C21 C C8 N Y N 0 -2.333 -0.464 -0.307
9 C24 C C9 N Y N 0 -3.773 1.721 0.48
10 C26 C C10 N Y N 0 -1.654 0.693 0.056
11 C28 C C11 N Y N 0 -6.668 1.396 -0.479
12 O13 O O1 N N N 0 0.277 2.612 0.527
13 C12 C C12 N N N 0 0.642 1.488 0.238
14 N11 N N1 N N N 0 1.957 1.195 0.204
15 C9 C C13 N Y N 0 4.329 1.622 0.49
16 C38 C C14 N Y N 0 4.903 0.95 1.553
17 C39 C C15 N Y N 0 6.176 0.425 1.432
18 S3 S S1 N N N 0 8.493 -0.106 0.091
19 O4 O O2 N N N 0 9.117 0.702 -0.897
20 O5 O O3 N N N 0 8.987 -0.146 1.423
21 C2 C C16 N N N 0 8.223 -1.786 -0.538
22 C1 C C17 N N N 0 9.572 -2.486 -0.718
23 N14 N N2 N N N 0 -0.268 0.536 -0.048
24 C16 C C18 N N N 0 -1.31 -1.497 -0.692
25 C19 C C19 N N N 0 -0.749 -3.843 -0.686
26 C18 C C20 N N N 0 -1.167 -3.488 -2.129
27 C25 C C21 N Y N 0 -2.396 1.809 0.459
28 C23 C C22 N Y N 0 -4.383 0.526 0.103
29 N22 N N3 N Y N 0 -3.651 -0.513 -0.273
30 C27 C C23 N Y N 0 -5.861 0.415 0.123
31 C34 C C24 N Y N 0 -6.491 -0.664 0.74
32 C35 C C25 N N N 0 -5.679 -1.747 1.403
33 C37 C C26 N N N 0 -5.919 -3.188 0.95
34 C36 C C27 N N N 0 -6.418 -2.724 2.32
35 N33 N N4 N Y N 0 -7.813 -0.724 0.736
36 C32 C C28 N Y N 0 -8.536 0.216 0.16
37 N31 N N5 N Y N 0 -7.986 1.258 -0.431
38 O29 O O4 N N N 0 -6.108 2.467 -1.093
39 C30 C C29 N N N 0 -7.0 3.42 -1.674
40 H1 H H1 N N N 0 6.845 1.354 -1.741
41 H2 H H2 N N N 0 4.578 2.292 -1.525
42 H3 H H3 N N N 0 2.852 3.08 -0.01
43 H4 H H4 N N N 0 2.76 2.473 1.661
44 H5 H H5 N N N 0 0.579 -0.779 -1.466
45 H6 H H6 N N N 0 0.642 -1.35 0.229
46 H7 H H7 N N N 0 -2.55 -1.84 -2.432
47 H8 H H8 N N N 0 -0.847 -1.449 -2.805
48 H9 H H9 N N N 0 -0.884 -2.62 1.125
49 H10 H H10 N N N 0 -2.469 -3.0 0.375
50 H11 H H11 N N N 0 -4.371 2.567 0.787
51 H12 H H12 N N N 0 2.252 0.322 -0.097
52 H13 H H13 N N N 0 4.357 0.837 2.478
53 H14 H H14 N N N 0 6.623 -0.103 2.261
54 H15 H H15 N N N 0 7.615 -2.347 0.172
55 H16 H H16 N N N 0 7.709 -1.736 -1.497
56 H17 H H17 N N N 0 10.18 -1.926 -1.428
57 H18 H H18 N N N 0 10.087 -2.536 0.241
58 H19 H H19 N N N 0 9.41 -3.496 -1.096
59 H20 H H20 N N N 0 0.335 -3.798 -0.581
60 H21 H H21 N N N 0 -1.119 -4.832 -0.414
61 H22 H H22 N N N 0 -2.041 -4.072 -2.419
62 H23 H H23 N N N 0 -0.343 -3.682 -2.815
63 H24 H H24 N N N 0 -1.899 2.724 0.747
64 H25 H H25 N N N 0 -4.661 -1.469 1.679
65 H26 H H26 N N N 0 -6.665 -3.353 0.172
66 H27 H H27 N N N 0 -5.06 -3.859 0.928
67 H28 H H28 N N N 0 -5.887 -3.089 3.199
68 H29 H H29 N N N 0 -7.492 -2.583 2.444
69 H30 H H30 N N N 0 -9.612 0.132 0.177
70 H31 H H31 N N N 0 -7.609 2.932 -2.435
71 H32 H H32 N N N 0 -7.647 3.832 -0.9
72 H33 H H33 N N N 0 -6.424 4.225 -2.131



9GS : Chemical Bonds

Total Number of Bonds: 77
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C10 N11 C N sing 1.47 N N
2 C10 C9 C C sing 1.51 N N
3 C8 C9 C C doub 1.38 N Y
4 C8 C7 C C sing 1.38 N Y
5 N11 C12 N C sing 1.35 N N
6 O13 C12 O C doub 1.22 N N
7 C9 C38 C C sing 1.38 N Y
8 C12 N14 C N sing 1.35 N N
9 C7 C6 C C doub 1.38 N Y
10 N14 C15 N C sing 1.47 N N
11 N14 C26 N C sing 1.4 N N
12 C25 C26 C C doub 1.4 N Y
13 C25 C24 C C sing 1.38 N Y
14 C15 C16 C C sing 1.53 N N
15 C26 C21 C C sing 1.39 N Y
16 C38 C39 C C doub 1.38 N Y
17 C6 C39 C C sing 1.38 N Y
18 C6 S3 C S sing 1.76 N N
19 C20 C16 C C sing 1.54 N N
20 C20 C19 C C sing 1.55 N N
21 C36 C35 C C sing 1.53 N N
22 C36 C37 C C sing 1.53 N N
23 C35 C37 C C sing 1.53 N N
24 C35 C34 C C sing 1.51 N N
25 C24 C23 C C doub 1.39 N Y
26 O5 S3 O S doub 1.42 N N
27 C21 C16 C C sing 1.5 N N
28 C21 N22 C N doub 1.32 N Y
29 C16 C17 C C sing 1.53 N N
30 C23 N22 C N sing 1.33 N Y
31 C23 C27 C C sing 1.48 N N
32 S3 C2 S C sing 1.81 N N
33 S3 O4 S O doub 1.42 N N
34 C19 C18 C C sing 1.54 N N
35 C34 C27 C C doub 1.39 N Y
36 C34 N33 C N sing 1.32 N Y
37 C2 C1 C C sing 1.53 N N
38 C27 C28 C C sing 1.41 N Y
39 C17 C18 C C sing 1.54 N N
40 N33 C32 N C doub 1.32 N Y
41 C28 O29 C O sing 1.36 N N
42 C28 N31 C N doub 1.33 N Y
43 C32 N31 C N sing 1.32 N Y
44 O29 C30 O C sing 1.43 N N
45 C7 H1 C H sing 1.08 N N
46 C8 H2 C H sing 1.08 N N
47 C10 H3 C H sing 1.09 N N
48 C10 H4 C H sing 1.09 N N
49 C15 H5 C H sing 1.09 N N
50 C15 H6 C H sing 1.09 N N
51 C17 H7 C H sing 1.09 N N
52 C17 H8 C H sing 1.09 N N
53 C20 H9 C H sing 1.09 N N
54 C20 H10 C H sing 1.09 N N
55 C24 H11 C H sing 1.08 N N
56 N11 H12 N H sing 0.97 N N
57 C38 H13 C H sing 1.08 N N
58 C39 H14 C H sing 1.08 N N
59 C2 H15 C H sing 1.09 N N
60 C2 H16 C H sing 1.09 N N
61 C1 H17 C H sing 1.09 N N
62 C1 H18 C H sing 1.09 N N
63 C1 H19 C H sing 1.09 N N
64 C19 H20 C H sing 1.09 N N
65 C19 H21 C H sing 1.09 N N
66 C18 H22 C H sing 1.09 N N
67 C18 H23 C H sing 1.09 N N
68 C25 H24 C H sing 1.08 N N
69 C35 H25 C H sing 1.09 N N
70 C37 H26 C H sing 1.09 N N
71 C37 H27 C H sing 1.09 N N
72 C36 H28 C H sing 1.09 N N
73 C36 H29 C H sing 1.09 N N
74 C32 H30 C H sing 1.08 N N
75 C30 H31 C H sing 1.09 N N
76 C30 H32 C H sing 1.09 N N
77 C30 H33 C H sing 1.09 N N



9GS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9GS 5vql Open in New Window Bound ligand 1 1