Chemical Components in the PDB

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GD9 : Summary

Code

GD9

One-letter code

X

Molecule name

2-(1H-indazol-4-yl)-6-{[4-(methylsulfonyl)piperazin-1-yl]methyl}-4-morpholin-4-yl-thieno[3,2-d]pyrimidine

Systematic names

ProgramVersionName
ACDLabs 10.04 2-(1H-indazol-4-yl)-6-{[4-(methylsulfonyl)piperazin-1-yl]methyl}-4-morpholin-4-ylthieno[3,2-d]pyrimidine
OpenEye OEToolkits 1.5.0 2-(1H-indazol-4-yl)-6-[(4-methylsulfonylpiperazin-1-yl)methyl]-4-morpholin-4-yl-thieno[2,3-e]pyrimidine

Formula

C23 H27 N7 O3 S2

Formal charge

0

Molecular weight

513.636 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=S(=O)(N1CCN(CC1)Cc3sc2c(nc(nc2c3)c5cccc4nncc45)N6CCOCC6)C
SMILES CACTVS 3.341 C[S](=O)(=O)N1CCN(CC1)Cc2sc3c(c2)nc(nc3N4CCOCC4)c5cccc6[nH]ncc56
SMILES OpenEye OEToolkits 1.5.0 CS(=O)(=O)N1CCN(CC1)Cc2cc3c(s2)c(nc(n3)c4cccc5c4cn[nH]5)N6CCOCC6
Canonical SMILES CACTVS 3.341 C[S](=O)(=O)N1CCN(CC1)Cc2sc3c(c2)nc(nc3N4CCOCC4)c5cccc6[nH]ncc56
Canonical SMILES OpenEye OEToolkits 1.5.0 CS(=O)(=O)N1CCN(CC1)Cc2cc3c(s2)c(nc(n3)c4cccc5c4cn[nH]5)N6CCOCC6

IUPAC InChI

InChI=1S/C23H27N7O3S2/c1-35(31,32)30-7-5-28(6-8-30)15-16-13-20-21(34-16)23(29-9-11-33-12-10-29)26-22(25-20)17-3-2-4-19-18(17)14-24-27-19/h2-4,13-14H,5-12,15H2,1H3,(H,24,27)

IUPAC InChI key

LHNIIDJUOCFXAP-UHFFFAOYSA-N
GD9

wwPDB Information

Atom count

62 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-06-03

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



GD9 : Atoms of Molecule

Total Number of Atoms: 62
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -1.086 0.856 0.876
2 C10 C C10 N N N 0 5.272 -2.13 0.337
3 C11 C C11 N N N 0 4.308 -0.127 -0.86
4 C12 C C12 N N N 0 3.505 0.182 0.408
5 C13 C C13 N N N 0 7.225 -1.335 -2.568
6 C14 C C14 N N N 0 -3.292 3.634 -0.12
7 C15 C C15 N N N 0 -3.148 5.158 -0.102
8 C16 C C16 N N N 0 -0.783 4.957 -0.428
9 C17 C C17 N N N 0 -0.904 3.431 -0.45
10 C18 C C18 N Y N 0 -5.718 -0.116 -0.781
11 C19 C C19 N Y N 0 -6.907 -0.698 -1.192
12 C2 C C2 N Y N 0 -1.237 -0.532 0.916
13 C20 C C20 N Y N 0 -7.065 -2.066 -1.174
14 C21 C C21 N Y N 0 -6.025 -2.884 -0.739
15 C22 C C22 N Y N 0 -4.81 -2.308 -0.324
16 C23 C C23 N Y N 0 -3.956 -3.371 0.048
17 C3 C C3 N Y N 0 -3.396 -0.28 0.095
18 C4 C C4 N Y N 0 -2.161 1.643 0.424
19 C5 C C5 N Y N 0 0.953 -0.381 1.714
20 C6 C C6 N Y N 0 -0.043 -1.193 1.4
21 C7 C C7 N N N 0 2.29 -0.839 2.237
22 C8 C C8 N Y N 0 -4.665 -0.905 -0.343
23 C9 C C9 N N N 0 4.432 -1.742 1.558
24 H10 H H10 N N N 0 6.235 -2.522 0.665
25 H10A H H10A N N N 0 4.745 -2.885 -0.246
26 H11 H H11 N N N 0 3.688 -0.69 -1.558
27 H11A H H11A N N N 0 4.633 0.804 -1.324
28 H12 H H12 N N N 0 4.09 0.831 1.059
29 H12A H H12A N N N 0 2.574 0.68 0.137
30 H13 H H13 N N N 0 7.139 -2.412 -2.422
31 H13A H H13A N N N 0 6.459 -1.0 -3.267
32 H13B H H13B N N N 0 8.211 -1.1 -2.969
33 H14 H H14 N N N 0 -3.481 3.299 -1.14
34 H14A H H14A N N N 0 -4.123 3.339 0.52
35 H15 H H15 N N N 0 -3.012 5.498 0.925
36 H15A H H15A N N N 0 -4.044 5.614 -0.522
37 H16 H H16 N N N 0 0.03 5.267 -1.084
38 H16A H H16A N N N 0 -0.579 5.291 0.589
39 H17 H H17 N N N 0 0.0080 2.987 -0.051
40 H17A H H17A N N N 0 -1.055 3.092 -1.475
41 H18 H H18 N N N 0 -5.611 0.959 -0.801
42 H19 H H19 N N N 0 -7.719 -0.072 -1.531
43 H20 H H20 N N N 0 -7.997 -2.505 -1.497
44 H23 H H23 N N N 0 -2.947 -3.267 0.417
45 H6 H H6 N N N 0 0.029 -2.266 1.497
46 H7 H H7 N N N 0 2.707 -0.071 2.889
47 H7A H H7A N N N 0 2.163 -1.763 2.8
48 H9 H H9 N N N 0 4.173 -2.639 2.121
49 H9A H H9A N N N 0 5.003 -1.066 2.193
50 HN6 H HN6 N N N 0 -6.55 -4.91 -0.82
51 N1 N N1 N Y N 0 -2.413 -1.056 0.506
52 N2 N N2 N Y N 0 -3.283 1.045 0.051
53 N3 N N3 N N N 0 -2.05 3.023 0.375
54 N4 N N4 N N N 0 3.203 -1.073 1.11
55 N5 N N5 N N N 0 5.483 -0.929 -0.486
56 N6 N N6 N Y N 0 -5.879 -4.241 -0.608
57 N7 N N7 N Y N 0 -4.594 -4.495 -0.113
58 O1 O O1 N N N 0 6.918 0.915 -1.166
59 O2 O O2 N N N 0 7.863 -1.047 0.0070
60 O3 O O3 N N N 0 -2.01 5.534 -0.883
61 S1 S S1 N Y N 0 0.52 1.296 1.437
62 S2 S S2 N N N 0 7.002 -0.491 -0.977



GD9 : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C15 O C sing 1.43 N N
2 O3 C16 O C sing 1.43 N N
3 C4 N2 C N doub 1.32 N Y
4 C4 N3 C N sing 1.39 N N
5 C4 C1 C C sing 1.41 N Y
6 C5 C6 C C doub 1.32 N Y
7 C5 C7 C C sing 1.51 N N
8 C5 S1 C S sing 1.75 N Y
9 C6 C2 C C sing 1.45 N Y
10 N1 C2 N C sing 1.35 N Y
11 N1 C3 N C doub 1.32 N Y
12 C7 N4 C N sing 1.47 N N
13 C8 C3 C C sing 1.48 N Y
14 C8 C18 C C doub 1.39 N Y
15 C8 C22 C C sing 1.41 N Y
16 N2 C3 N C sing 1.33 N Y
17 C9 C10 C C sing 1.53 N N
18 C9 N4 C N sing 1.47 N N
19 C10 N5 C N sing 1.47 N N
20 C11 C12 C C sing 1.53 N N
21 C11 N5 C N sing 1.47 N N
22 C12 N4 C N sing 1.47 N N
23 N3 C14 N C sing 1.47 N N
24 N3 C17 N C sing 1.47 N N
25 C13 S2 C S sing 1.81 N N
26 C14 C15 C C sing 1.53 N N
27 O2 S2 O S doub 1.42 N N
28 S2 O1 S O doub 1.42 N N
29 S2 N5 S N sing 1.66 N N
30 S1 C1 S C sing 1.76 N Y
31 C2 C1 C C doub 1.4 N Y
32 C18 C19 C C sing 1.39 N Y
33 C19 C20 C C doub 1.38 N Y
34 C20 C21 C C sing 1.39 N Y
35 C21 N6 C N sing 1.37 N Y
36 C21 C22 C C doub 1.41 N Y
37 N6 N7 N N sing 1.4 N Y
38 C22 C23 C C sing 1.41 N Y
39 C23 N7 C N doub 1.3 N Y
40 C16 C17 C C sing 1.53 N N
41 C6 H6 C H sing 1.08 N N
42 C7 H7 C H sing 1.09 N N
43 C7 H7A C H sing 1.09 N N
44 C9 H9 C H sing 1.09 N N
45 C9 H9A C H sing 1.09 N N
46 C10 H10 C H sing 1.09 N N
47 C10 H10A C H sing 1.09 N N
48 C11 H11 C H sing 1.09 N N
49 C11 H11A C H sing 1.09 N N
50 C12 H12 C H sing 1.09 N N
51 C12 H12A C H sing 1.09 N N
52 C13 H13 C H sing 1.09 N N
53 C13 H13A C H sing 1.09 N N
54 C13 H13B C H sing 1.09 N N
55 C14 H14 C H sing 1.09 N N
56 C14 H14A C H sing 1.09 N N
57 C15 H15 C H sing 1.09 N N
58 C15 H15A C H sing 1.09 N N
59 C18 H18 C H sing 1.08 N N
60 C19 H19 C H sing 1.08 N N
61 C20 H20 C H sing 1.08 N N
62 N6 HN6 N H sing 0.97 N N
63 C23 H23 C H sing 1.08 N N
64 C16 H16 C H sing 1.09 N N
65 C16 H16A C H sing 1.09 N N
66 C17 H17 C H sing 1.09 N N
67 C17 H17A C H sing 1.09 N N



GD9 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
GD9 2wxp Open in New Window Bound ligand 1 1
GD9 2y3a Open in New Window Bound ligand 1 1
GD9 3dbs Open in New Window Bound ligand 1 1