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406 : Summary

Code

406

One-letter code

X

Molecule name

N-[3-(4,5'-BIPYRIMIDIN-2-YLAMINO)-4-METHYLPHENYL]-4-{[(3S)-3-(DIMETHYLAMINO)PYRROLIDIN-1-YL]METHYL}-3-(TRIFLUOROMETHYL) BENZAMIDE

Synonyms

INNO-406

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[3-(4,5'-bipyrimidin-2-ylamino)-4-methylphenyl]-4-{[(3S)-3-(dimethylamino)pyrrolidin-1-yl]methyl}-3-(trifluoromethyl)benzamide
OpenEye OEToolkits 1.5.0 4-[[(1S,3S)-3-dimethylaminopyrrolidin-1-yl]methyl]-N-[4-methyl-3-[(4-pyrimidin-5-ylpyrimidin-2-yl)amino]phenyl]-3-(trifluoromethyl)benzamide

Formula

C30 H31 F3 N8 O

Formal charge

0

Molecular weight

576.615 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 FC(F)(F)c4cc(C(=O)Nc3ccc(c(Nc2nc(c1cncnc1)ccn2)c3)C)ccc4CN5CCC(N(C)C)C5
SMILES CACTVS 3.341 CN(C)[CH]1CCN(C1)Cc2ccc(cc2C(F)(F)F)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cncnc5)c3
SMILES OpenEye OEToolkits 1.5.0 Cc1ccc(cc1Nc2nccc(n2)c3cncnc3)NC(=O)c4ccc(c(c4)C(F)(F)F)CN5CCC(C5)N(C)C
Canonical SMILES CACTVS 3.341 CN(C)[C@H]1CCN(C1)Cc2ccc(cc2C(F)(F)F)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cncnc5)c3
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1ccc(cc1Nc2nccc(n2)c3cncnc3)NC(=O)c4ccc(c(c4)C(F)(F)F)C[N@@]5CC[C@@H](C5)N(C)C

IUPAC InChI

InChI=1S/C30H31F3N8O/c1-19-4-7-23(13-27(19)39-29-36-10-8-26(38-29)22-14-34-18-35-15-22)37-28(42)20-5-6-21(25(12-20)30(31,32)33)16-41-11-9-24(17-41)40(2)3/h4-8,10,12-15,18,24H,9,11,16-17H2,1-3H3,(H,37,42)(H,36,38,39)/t24-/m0/s1

IUPAC InChI key

ZGBAJMQHJDFTQJ-DEOSSOPVSA-N
406

wwPDB Information

Atom count

73 (42 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-11-13

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



406 : Atoms of Molecule

Total Number of Atoms: 73
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 -4.068 -4.324 -0.451
2 C2 C C2 N Y N 0 -3.406 -3.111 -0.266
3 C3 C C3 N Y N 0 -2.02 -3.089 -0.11
4 C4 C C4 N Y N 0 -1.304 -4.281 -0.14
5 C5 C C5 N Y N 0 -1.958 -5.495 -0.325
6 C6 C C6 N Y N 0 -3.344 -5.516 -0.48
7 C7 C C7 N N N 0 -1.204 -6.784 -0.359
8 F8 F F8 N N N 0 -2.0 -7.876 -0.548
9 F9 F F9 N N N 0 -0.273 -6.843 -1.355
10 F10 F F10 N N N 0 -0.521 -7.021 0.798
11 C11 C C11 N N N 0 0.187 -4.233 0.029
12 N12 N N12 R N N 0 0.876 -4.093 -1.244
13 C13 C C13 N N N 0 2.334 -4.044 -1.097
14 C14 C C14 N N N 0 2.831 -3.277 -2.323
15 C15 C C15 S N N 0 1.56 -2.84 -3.051
16 C16 C C16 N N N 0 0.502 -2.869 -1.956
17 N17 N N17 N N N 0 1.686 -1.539 -3.684
18 C18 C C18 N N N 0 0.442 -1.17 -4.366
19 C19 C C19 N N N 0 2.802 -1.528 -4.634
20 N20 N N20 N Y N 0 -6.783 -10.328 -1.433
21 C21 C C21 N Y N 0 -6.002 -9.669 -2.311
22 N22 N N22 N Y N 0 -6.258 -8.48 -2.888
23 C23 C C23 N Y N 0 -7.429 -7.913 -2.529
24 C24 C C24 N Y N 0 -8.314 -8.485 -1.641
25 C25 C C25 N Y N 0 -7.937 -9.704 -1.118
26 C26 C C26 N Y N 0 -9.558 -7.847 -1.28
27 N27 N N27 N Y N 0 -9.541 -6.498 -1.315
28 C28 C C28 N Y N 0 -10.703 -5.902 -0.978
29 N29 N N29 N Y N 0 -11.849 -6.518 -0.621
30 C30 C C30 N Y N 0 -11.795 -7.866 -0.608
31 C31 C C31 N Y N 0 -10.666 -8.591 -0.931
32 N32 N N32 N N N 0 -10.722 -4.495 -1.002
33 C33 C C33 N Y N 0 -8.396 -3.824 -1.081
34 C34 C C34 N Y N 0 -7.435 -2.879 -1.392
35 C35 C C35 N Y N 0 -7.772 -1.652 -1.934
36 C36 C C36 N Y N 0 -9.115 -1.359 -2.173
37 C37 C C37 N Y N 0 -10.099 -2.299 -1.865
38 C38 C C38 N Y N 0 -9.739 -3.532 -1.319
39 C39 C C39 N N N 0 -11.529 -1.96 -2.13
40 N40 N N40 N N N 0 -6.069 -3.176 -1.15
41 C41 C C41 N N N 0 -5.513 -4.347 -0.613
42 O42 O O42 N N N 0 -6.192 -5.322 -0.264
43 H391 H 1H39 N N N 0 -12.083 -2.858 -2.427
44 H392 H 2H39 N N N 0 -12.007 -1.532 -1.24
45 H393 H 3H39 N N N 0 -11.617 -1.214 -2.93
46 H36 H H36 N N N 0 -9.385 -0.396 -2.598
47 H35 H H35 N N N 0 -7.014 -0.912 -2.178
48 H33 H H33 N N N 0 -8.116 -4.785 -0.656
49 H32 H H32 N N N 0 -11.616 -4.091 -0.742
50 H30 H H30 N N N 0 -12.715 -8.364 -0.321
51 H31 H H31 N N N 0 -10.666 -9.674 -0.909
52 H25 H H25 N N N 0 -8.563 -10.239 -0.41
53 H21 H H21 N N N 0 -5.068 -10.147 -2.581
54 H23 H H23 N N N 0 -7.629 -6.954 -2.998
55 H40 H H40 N N N 0 -5.407 -2.445 -1.398
56 H2 H H2 N N N 0 -3.96 -2.176 -0.241
57 H3 H H3 N N N 0 -1.513 -2.138 0.033
58 H111 H 1H11 N N N 0 0.476 -3.388 0.664
59 H112 H 2H11 N N N 0 0.558 -5.143 0.512
60 H131 H 1H13 N N N 0 2.758 -5.052 -1.057
61 H132 H 2H13 N N N 0 2.639 -3.507 -0.189
62 H141 H 1H14 N N N 0 3.432 -2.418 -2.001
63 H142 H 2H14 N N N 0 3.458 -3.899 -2.971
64 H15 H H15 N N N 0 1.313 -3.587 -3.818
65 H161 H 1H16 N N N 0 0.572 -1.986 -1.308
66 H162 H 2H16 N N N 0 -0.51 -2.926 -2.37
67 H181 H 1H18 N N N 0 -0.4 -1.231 -3.671
68 H182 H 2H18 N N N 0 0.255 -1.845 -5.205
69 H183 H 3H18 N N N 0 0.509 -0.147 -4.748
70 H191 H 1H19 N N N 0 3.745 -1.37 -4.104
71 H192 H 2H19 N N N 0 2.67 -0.725 -5.364
72 H193 H 3H19 N N N 0 2.854 -2.481 -5.168
73 H6 H H6 N N N 0 -3.859 -6.463 -0.624



406 : 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 C1 C41 C C sing 1.45 N N
2 C1 C2 C C sing 1.39 N Y
3 C1 C6 C C doub 1.39 N Y
4 C2 C3 C C doub 1.39 N Y
5 C2 H2 C H sing 1.09 N N
6 C3 C4 C C sing 1.39 N Y
7 C3 H3 C H sing 1.09 N N
8 C4 C11 C C sing 1.5 N N
9 C4 C5 C C doub 1.39 N Y
10 C5 C6 C C sing 1.39 N Y
11 C5 C7 C C sing 1.49 N N
12 C6 H6 C H sing 1.09 N N
13 C7 F8 C F sing 1.36 N N
14 C7 F9 C F sing 1.36 N N
15 C7 F10 C F sing 1.36 N N
16 C11 N12 C N sing 1.45 N N
17 C11 H111 C H sing 1.1 N N
18 C11 H112 C H sing 1.1 N N
19 N12 C13 N C sing 1.47 N N
20 N12 C16 N C sing 1.46 N N
21 C13 C14 C C sing 1.53 N N
22 C13 H131 C H sing 1.09 N N
23 C13 H132 C H sing 1.1 N N
24 C14 C15 C C sing 1.53 N N
25 C14 H141 C H sing 1.1 N N
26 C14 H142 C H sing 1.1 N N
27 C15 C16 C C sing 1.52 N N
28 C15 N17 C N sing 1.45 N N
29 C15 H15 C H sing 1.1 N N
30 C16 H161 C H sing 1.1 N N
31 C16 H162 C H sing 1.09 N N
32 N17 C18 N C sing 1.47 N N
33 N17 C19 N C sing 1.47 N N
34 C18 H181 C H sing 1.09 N N
35 C18 H182 C H sing 1.09 N N
36 C18 H183 C H sing 1.09 N N
37 C19 H191 C H sing 1.09 N N
38 C19 H192 C H sing 1.09 N N
39 C19 H193 C H sing 1.09 N N
40 N20 C25 N C sing 1.35 N Y
41 N20 C21 N C doub 1.35 N Y
42 C21 N22 C N sing 1.35 N Y
43 C21 H21 C H sing 1.08 N N
44 N22 C23 N C doub 1.35 N Y
45 C23 C24 C C sing 1.38 N Y
46 C23 H23 C H sing 1.09 N N
47 C24 C26 C C sing 1.44 N Y
48 C24 C25 C C doub 1.38 N Y
49 C25 H25 C H sing 1.09 N N
50 C26 C31 C C doub 1.38 N Y
51 C26 N27 C N sing 1.35 N Y
52 N27 C28 N C doub 1.35 N Y
53 C28 N32 C N sing 1.41 N N
54 C28 N29 C N sing 1.35 N Y
55 N29 C30 N C doub 1.35 N Y
56 C30 C31 C C sing 1.38 N Y
57 C30 H30 C H sing 1.08 N N
58 C31 H31 C H sing 1.08 N N
59 N32 C38 N C sing 1.41 N N
60 N32 H32 N H sing 1.01 N N
61 C33 C34 C C sing 1.38 N Y
62 C33 C38 C C doub 1.39 N Y
63 C33 H33 C H sing 1.09 N N
64 C34 C35 C C doub 1.38 N Y
65 C34 N40 C N sing 1.42 N N
66 C35 C36 C C sing 1.4 N Y
67 C35 H35 C H sing 1.09 N N
68 C36 C37 C C doub 1.4 N Y
69 C36 H36 C H sing 1.09 N N
70 C37 C39 C C sing 1.49 N N
71 C37 C38 C C sing 1.4 N Y
72 C39 H391 C H sing 1.1 N N
73 C39 H392 C H sing 1.1 N N
74 C39 H393 C H sing 1.1 N N
75 N40 C41 N C sing 1.4 N N
76 N40 H40 N H sing 1.02 N N
77 C41 O42 C O doub 1.24 N N



406 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
406 2e2b Open in New Window Bound ligand 2 1