Chemical Components in the PDB

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8JC : Summary

Code

8JC

One-letter code

X

Molecule name

N-[3-[[2-[[4-(4-ethanoylpiperazin-1-yl)-2-methoxy-phenyl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]amino]phenyl]prop-2-enamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 ~{N}-[3-[[2-[[4-(4-ethanoylpiperazin-1-yl)-2-methoxy-phenyl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]amino]phenyl]prop-2-enamide

Formula

C27 H28 F3 N7 O3

Formal charge

0

Molecular weight

555.552 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COc1cc(ccc1Nc2ncc(c(Nc3cccc(NC(=O)C=C)c3)n2)C(F)(F)F)N4CCN(CC4)C(C)=O
SMILES OpenEye OEToolkits 2.0.6 CC(=O)N1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc(c(n3)Nc4cccc(c4)NC(=O)C=C)C(F)(F)F
Canonical SMILES CACTVS 3.385 COc1cc(ccc1Nc2ncc(c(Nc3cccc(NC(=O)C=C)c3)n2)C(F)(F)F)N4CCN(CC4)C(C)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CC(=O)N1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc(c(n3)Nc4cccc(c4)NC(=O)C=C)C(F)(F)F

IUPAC InChI

InChI=1S/C27H28F3N7O3/c1-4-24(39)32-18-6-5-7-19(14-18)33-25-21(27(28,29)30)16-31-26(35-25)34-22-9-8-20(15-23(22)40-3)37-12-10-36(11-13-37)17(2)38/h4-9,14-16H,1,10-13H2,2-3H3,(H,32,39)(H2,31,33,34,35)

IUPAC InChI key

HUFOZJXAKZVRNJ-UHFFFAOYSA-N
8JC

wwPDB Information

Atom count

68 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-07-14

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



8JC : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -2.465 1.015 -0.327
2 C5 C C2 N Y N 0 -1.836 2.26 -0.403
3 C6 C C3 N Y N 0 -0.457 2.306 -0.334
4 N1 N N1 N Y N 0 0.224 1.177 -0.2
5 N3 N N2 N Y N 0 -1.72 -0.077 -0.193
6 C2 C C4 N Y N 0 -0.4 0.01 -0.131
7 CAA C C5 N N N 0 2.913 -4.225 -1.268
8 CAB C C6 N N N 0 10.271 0.552 -1.158
9 CAK C C7 N Y N 0 -4.451 -2.627 -1.14
10 CAL C C8 N Y N 0 -5.671 -2.826 -0.524
11 CAM C C9 N Y N 0 -3.845 -1.386 -1.096
12 CAN C C10 N Y N 0 3.663 0.124 0.979
13 CAO C C11 N Y N 0 2.294 0.045 0.8
14 CAQ C C12 N Y N 0 -5.692 -0.528 0.182
15 CAR C C13 N Y N 0 3.927 -2.029 -0.062
16 CAS C C14 N N N 0 -10.609 -0.177 1.52
17 CAT C C15 N N N 0 -9.708 -1.155 1.507
18 CAU C C16 N N N 0 7.733 0.409 1.72
19 CAV C C17 N N N 0 8.08 -1.067 -0.298
20 CAW C C18 N N N 0 6.238 0.434 1.383
21 CAX C C19 N N N 0 6.572 -0.984 -0.556
22 CBG C C20 N N N 0 9.515 0.882 0.103
23 CBH C C21 N N N 0 -8.448 -0.984 0.768
24 CBI C C22 N Y N 0 -6.295 -1.776 0.139
25 CBJ C C23 N Y N 0 -4.461 -0.334 -0.43
26 CBK C C24 N Y N 0 4.482 -0.91 0.546
27 CBM C C25 N Y N 0 1.737 -1.067 0.189
28 CBN C C26 N Y N 0 2.557 -2.106 -0.247
29 CBT C C27 N N N 0 -2.643 3.523 -0.555
30 FAG F F1 N N N 0 -1.781 4.624 -0.606
31 FAH F F2 N N N 0 -3.389 3.46 -1.737
32 FAI F F3 N N N 0 -3.508 3.659 0.536
33 NBB N N3 N N N 0 -7.535 -1.976 0.755
34 NBC N N4 N N N 0 -3.847 0.921 -0.386
35 NBD N N5 N N N 0 0.348 -1.147 0.008
36 NBR N N6 N N N 0 8.484 0.105 0.493
37 NBS N N7 N N N 0 5.867 -0.825 0.723
38 OAE O O1 N N N 0 9.834 1.845 0.768
39 OAF O O2 N N N 0 -8.229 0.052 0.17
40 OBE O O3 N N N 0 2.012 -3.198 -0.847
41 H1 H H1 N N N 0 0.06 3.252 -0.39
42 H2 H H2 N N N 0 3.619 -3.815 -1.99
43 H3 H H3 N N N 0 3.457 -4.607 -0.404
44 H4 H H4 N N N 0 2.349 -5.035 -1.73
45 H5 H H5 N N N 0 9.588 0.575 -2.007
46 H6 H H6 N N N 0 11.063 1.286 -1.309
47 H7 H H7 N N N 0 10.708 -0.442 -1.07
48 H8 H H8 N N N 0 -3.968 -3.445 -1.655
49 H9 H H9 N N N 0 -6.14 -3.798 -0.558
50 H10 H H10 N N N 0 -2.891 -1.234 -1.58
51 H11 H H11 N N N 0 4.096 0.993 1.451
52 H12 H H12 N N N 0 1.659 0.85 1.138
53 H13 H H13 N N N 0 -6.175 0.29 0.696
54 H14 H H14 N N N 0 4.564 -2.833 -0.399
55 H15 H H15 N N N 0 -11.534 -0.302 2.063
56 H16 H H16 N N N 0 -10.415 0.743 0.989
57 H18 H H18 N N N 0 -9.902 -2.075 2.039
58 H20 H H20 N N N 0 8.037 1.382 2.105
59 H21 H H21 N N N 0 7.929 -0.359 2.469
60 H22 H H22 N N N 0 8.307 -1.978 0.255
61 H23 H H23 N N N 0 8.615 -1.073 -1.248
62 H24 H H24 N N N 0 5.66 0.548 2.3
63 H25 H H25 N N N 0 6.03 1.269 0.715
64 H26 H H26 N N N 0 6.359 -0.128 -1.197
65 H27 H H27 N N N 0 6.236 -1.898 -1.046
66 H28 H H28 N N N 0 -7.738 -2.828 1.171
67 H29 H H29 N N N 0 -4.388 1.726 -0.395
68 H30 H H30 N N N 0 -0.089 -2.013 -0.019



8JC : 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 FAI CBT F C sing 1.4 N N
2 FAH CBT F C sing 1.4 N N
3 FAG CBT F C sing 1.4 N N
4 CBT C5 C C sing 1.51 N N
5 C5 C6 C C doub 1.38 N Y
6 C5 C4 C C sing 1.4 N Y
7 C6 N1 C N sing 1.33 N Y
8 NBC C4 N C sing 1.39 N N
9 NBC CBJ N C sing 1.4 N N
10 C4 N3 C N doub 1.33 N Y
11 CBJ CAM C C doub 1.39 N Y
12 CBJ CAQ C C sing 1.39 N Y
13 CAM CAK C C sing 1.38 N Y
14 N1 C2 N C doub 1.33 N Y
15 CAQ CBI C C doub 1.39 N Y
16 OAF CBH O C doub 1.22 N N
17 N3 C2 N C sing 1.32 N Y
18 CAK CAL C C doub 1.38 N Y
19 C2 NBD C N sing 1.38 N N
20 CBI CAL C C sing 1.39 N Y
21 CBI NBB C N sing 1.4 N N
22 CBH NBB C N sing 1.35 N N
23 CBH CAT C C sing 1.47 N N
24 CAS CAT C C doub 1.33 N N
25 NBD CBM N C sing 1.4 N N
26 CAO CBM C C doub 1.39 N Y
27 CAO CAN C C sing 1.38 N Y
28 CBM CBN C C sing 1.39 N Y
29 CAN CBK C C doub 1.39 N Y
30 CBN OBE C O sing 1.36 N N
31 CBN CAR C C doub 1.38 N Y
32 OBE CAA O C sing 1.43 N N
33 CBK CAR C C sing 1.39 N Y
34 CBK NBS C N sing 1.4 N N
35 CAW NBS C N sing 1.47 N N
36 CAW CAU C C sing 1.53 N N
37 NBS CAX N C sing 1.47 N N
38 CAU NBR C N sing 1.47 N N
39 CAX CAV C C sing 1.53 N N
40 NBR CAV N C sing 1.47 N N
41 NBR CBG N C sing 1.35 N N
42 OAE CBG O C doub 1.21 N N
43 CBG CAB C C sing 1.51 N N
44 C6 H1 C H sing 1.08 N N
45 CAA H2 C H sing 1.09 N N
46 CAA H3 C H sing 1.09 N N
47 CAA H4 C H sing 1.09 N N
48 CAB H5 C H sing 1.09 N N
49 CAB H6 C H sing 1.09 N N
50 CAB H7 C H sing 1.09 N N
51 CAK H8 C H sing 1.08 N N
52 CAL H9 C H sing 1.08 N N
53 CAM H10 C H sing 1.08 N N
54 CAN H11 C H sing 1.08 N N
55 CAO H12 C H sing 1.08 N N
56 CAQ H13 C H sing 1.08 N N
57 CAR H14 C H sing 1.08 N N
58 CAS H15 C H sing 1.08 N N
59 CAS H16 C H sing 1.08 N N
60 CAT H18 C H sing 1.08 N N
61 CAU H20 C H sing 1.09 N N
62 CAU H21 C H sing 1.09 N N
63 CAV H22 C H sing 1.09 N N
64 CAV H23 C H sing 1.09 N N
65 CAW H24 C H sing 1.09 N N
66 CAW H25 C H sing 1.09 N N
67 CAX H26 C H sing 1.09 N N
68 CAX H27 C H sing 1.09 N N
69 NBB H28 N H sing 0.97 N N
70 NBC H29 N H sing 0.97 N N
71 NBD H30 N H sing 0.97 N N



8JC : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
8JC 5xdk Open in New Window Bound ligand 1 1
8JC 5xdl Open in New Window Bound ligand 1 1