Chemical Components in the PDB

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07J : Summary

Code

07J

One-letter code

X

Molecule name

3-(2,6-dichloro-3,5-dimethoxyphenyl)-1-(6-{[4-(4-ethylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)-1-methylurea

Synonyms

BGJ398

Systematic names

ProgramVersionName
ACDLabs 12.01 3-(2,6-dichloro-3,5-dimethoxyphenyl)-1-(6-{[4-(4-ethylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)-1-methylurea
OpenEye OEToolkits 1.7.2 3-[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]-1-[6-[[4-(4-ethylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]-1-methyl-urea

Formula

C26 H31 Cl2 N7 O3

Formal charge

0

Molecular weight

560.475 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Clc1c(OC)cc(OC)c(Cl)c1NC(=O)N(c2ncnc(c2)Nc4ccc(N3CCN(CC)CC3)cc4)C
SMILES CACTVS 3.370 CCN1CCN(CC1)c2ccc(Nc3cc(ncn3)N(C)C(=O)Nc4c(Cl)c(OC)cc(OC)c4Cl)cc2
SMILES OpenEye OEToolkits 1.7.2 CCN1CCN(CC1)c2ccc(cc2)Nc3cc(ncn3)N(C)C(=O)Nc4c(c(cc(c4Cl)OC)OC)Cl
Canonical SMILES CACTVS 3.370 CCN1CCN(CC1)c2ccc(Nc3cc(ncn3)N(C)C(=O)Nc4c(Cl)c(OC)cc(OC)c4Cl)cc2
Canonical SMILES OpenEye OEToolkits 1.7.2 CCN1CCN(CC1)c2ccc(cc2)Nc3cc(ncn3)N(C)C(=O)Nc4c(c(cc(c4Cl)OC)OC)Cl

IUPAC InChI

InChI=1S/C26H31Cl2N7O3/c1-5-34-10-12-35(13-11-34)18-8-6-17(7-9-18)31-21-15-22(30-16-29-21)33(2)26(36)32-25-23(27)19(37-3)14-20(38-4)24(25)28/h6-9,14-16H,5,10-13H2,1-4H3,(H,32,36)(H,29,30,31)

IUPAC InChI key

QADPYRIHXKWUSV-UHFFFAOYSA-N
07J

wwPDB Information

Atom count

69 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-09-27

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



07J : Atoms of Molecule

Total Number of Atoms: 69
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C10 N Y N 0 7.263 1.541 0.811
2 C11 C C11 N Y N 0 6.188 2.049 0.097
3 C13 C C13 N N N 0 7.094 4.216 0.468
4 C14 C C14 N Y N 0 5.234 1.189 -0.427
5 C17 C C17 N N N 0 2.555 -2.817 -1.815
6 C18 C C18 N Y N 0 0.809 -1.175 -1.203
7 C19 C C19 N Y N 0 -0.04 -1.621 -0.197
8 C2 C C2 N N N 0 3.076 -0.735 -0.661
9 C20 C C20 N Y N 0 -1.373 -1.222 -0.234
10 C22 C C22 N Y N 0 -0.947 -0.031 -2.16
11 C25 C C25 N Y N 0 -3.623 -1.335 0.633
12 C26 C C26 N Y N 0 -4.219 -1.27 -0.619
13 C27 C C27 N Y N 0 -5.562 -0.97 -0.731
14 C28 C C28 N Y N 0 -6.317 -0.734 0.41
15 C29 C C29 N Y N 0 -5.722 -0.799 1.663
16 C30 C C30 N Y N 0 -4.38 -1.104 1.775
17 C32 C C32 N N N 0 -8.282 -0.217 1.621
18 C33 C C33 N N N 0 -9.783 0.034 1.459
19 C35 C C35 N N N 0 -11.42 1.525 0.477
20 C36 C C36 N N N 0 -11.584 2.879 -0.215
21 C37 C C37 N N N 0 -9.388 0.993 -0.728
22 C38 C C38 N N N 0 -7.887 0.741 -0.566
23 C4 C C4 N Y N 0 5.35 -0.18 -0.226
24 C5 C C5 N Y N 0 6.426 -0.688 0.489
25 C7 C C7 N Y N 0 7.382 0.173 1.007
26 C9 C C9 N N N 0 9.383 0.621 2.211
27 CL1 CL CL1 N N N 0 6.576 -2.4 0.734
28 CL2 CL CL2 N N N 0 3.889 1.825 -1.321
29 H1 H H1 N N N 0 4.656 -1.877 -1.176
30 H10 H H10 N N N 0 1.87 -3.069 -2.625
31 H11 H H11 N N N 0 3.566 -2.725 -2.211
32 H12 H H12 N N N 0 0.325 -2.261 0.593
33 H13 H H13 N N N 0 -1.311 0.609 -2.95
34 H14 H H14 N N N 0 -1.938 -2.143 1.51
35 H15 H H15 N N N 0 -3.631 -1.454 -1.507
36 H16 H H16 N N N 0 -6.025 -0.919 -1.705
37 H17 H H17 N N N 0 -6.309 -0.615 2.551
38 H18 H H18 N N N 0 -3.918 -1.159 2.749
39 H19 H H19 N N N 0 -8.126 -1.102 2.238
40 H2 H H2 N N N 0 8.881 1.311 2.889
41 H20 H H20 N N N 0 -7.818 0.646 2.098
42 H21 H H21 N N N 0 -10.252 -0.84 1.007
43 H22 H H22 N N N 0 -10.228 0.22 2.437
44 H24 H H24 N N N 0 -11.917 0.753 -0.111
45 H25 H H25 N N N 0 -11.866 1.568 1.47
46 H26 H H26 N N N 0 -12.644 3.116 -0.303
47 H27 H H27 N N N 0 -11.086 3.65 0.373
48 H28 H H28 N N N 0 -11.138 2.836 -1.209
49 H29 H H29 N N N 0 -9.852 0.13 -1.205
50 H3 H H3 N N N 0 10.172 0.093 2.748
51 H30 H H30 N N N 0 -9.544 1.878 -1.345
52 H31 H H31 N N N 0 -7.418 1.615 -0.114
53 H32 H H32 N N N 0 -7.442 0.555 -1.544
54 H4 H H4 N N N 0 9.818 1.178 1.381
55 H5 H H5 N N N 0 8.007 2.211 1.215
56 H6 H H6 N N N 0 6.881 5.261 0.243
57 H7 H H7 N N N 0 7.121 4.076 1.548
58 H8 H H8 N N N 0 8.059 3.942 0.041
59 H9 H H9 N N N 0 2.531 -3.602 -1.06
60 N16 N N16 N N N 0 2.15 -1.546 -1.211
61 N21 N N21 N Y N 0 -1.784 -0.432 -1.225
62 N23 N N23 N Y N 0 0.322 -0.383 -2.156
63 N24 N N24 N N N 0 -2.261 -1.64 0.746
64 N3 N N3 N N N 0 4.384 -1.049 -0.75
65 N31 N N31 N N N 0 -7.679 -0.429 0.298
66 N34 N N34 N N N 0 -9.991 1.205 0.595
67 O1 O O1 N N N 0 2.732 0.277 -0.082
68 O12 O O12 N N N 0 6.072 3.39 -0.094
69 O8 O O8 N N N 0 8.437 -0.324 1.706



07J : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C13 O12 C O sing 1.43 N N
2 O12 C11 O C sing 1.36 N N
3 C11 C10 C C doub 1.39 N Y
4 C11 C14 C C sing 1.39 N Y
5 CL2 C14 CL C sing 1.74 N N
6 C10 C7 C C sing 1.39 N Y
7 C14 C4 C C doub 1.39 N Y
8 C9 O8 C O sing 1.43 N N
9 C7 O8 C O sing 1.36 N N
10 C7 C5 C C doub 1.39 N Y
11 O1 C2 O C doub 1.22 N N
12 C4 C5 C C sing 1.39 N Y
13 C4 N3 C N sing 1.4 N N
14 C5 CL1 C CL sing 1.74 N N
15 C2 N3 C N sing 1.35 N N
16 C2 N16 C N sing 1.35 N N
17 C17 N16 C N sing 1.46 N N
18 N16 C18 N C sing 1.39 N N
19 C18 C19 C C doub 1.39 N Y
20 C18 N23 C N sing 1.33 N Y
21 C26 C27 C C doub 1.38 N Y
22 C26 C25 C C sing 1.39 N Y
23 C19 C20 C C sing 1.39 N Y
24 N23 C22 N C doub 1.32 N Y
25 C27 C28 C C sing 1.39 N Y
26 C38 C37 C C sing 1.53 N N
27 C38 N31 C N sing 1.47 N N
28 C37 N34 C N sing 1.47 N N
29 C20 N24 C N sing 1.39 N N
30 C20 N21 C N doub 1.33 N Y
31 C22 N21 C N sing 1.32 N Y
32 N24 C25 N C sing 1.4 N N
33 C25 C30 C C doub 1.39 N Y
34 N34 C35 N C sing 1.47 N N
35 N34 C33 N C sing 1.47 N N
36 C35 C36 C C sing 1.53 N N
37 C28 N31 C N sing 1.4 N N
38 C28 C29 C C doub 1.39 N Y
39 N31 C32 N C sing 1.47 N N
40 C32 C33 C C sing 1.53 N N
41 C30 C29 C C sing 1.38 N Y
42 N3 H1 N H sing 0.97 N N
43 C9 H2 C H sing 1.09 N N
44 C9 H3 C H sing 1.09 N N
45 C9 H4 C H sing 1.09 N N
46 C10 H5 C H sing 1.08 N N
47 C13 H6 C H sing 1.09 N N
48 C13 H7 C H sing 1.09 N N
49 C13 H8 C H sing 1.09 N N
50 C17 H9 C H sing 1.09 N N
51 C17 H10 C H sing 1.09 N N
52 C17 H11 C H sing 1.09 N N
53 C19 H12 C H sing 1.08 N N
54 C22 H13 C H sing 1.08 N N
55 N24 H14 N H sing 0.97 N N
56 C26 H15 C H sing 1.08 N N
57 C27 H16 C H sing 1.08 N N
58 C29 H17 C H sing 1.08 N N
59 C30 H18 C H sing 1.08 N N
60 C32 H19 C H sing 1.09 N N
61 C32 H20 C H sing 1.09 N N
62 C33 H21 C H sing 1.09 N N
63 C33 H22 C H sing 1.09 N N
64 C35 H24 C H sing 1.09 N N
65 C35 H25 C H sing 1.09 N N
66 C36 H26 C H sing 1.09 N N
67 C36 H27 C H sing 1.09 N N
68 C36 H28 C H sing 1.09 N N
69 C37 H29 C H sing 1.09 N N
70 C37 H30 C H sing 1.09 N N
71 C38 H31 C H sing 1.09 N N
72 C38 H32 C H sing 1.09 N N



07J : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
07J 3tt0 Open in New Window Bound ligand 2 1