Chemical Components in the PDB

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JAU : Summary

Code

JAU

One-letter code

X

Molecule name

5-chloranyl-N2-[3-chloranyl-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-N4-(2-dimethylphosphorylphenyl)pyrimidine-2,4-diamine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 5-chloranyl-~{N}2-[3-chloranyl-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-~{N}4-(2-dimethylphosphorylphenyl)pyrimidine-2,4-diamine

Formula

C28 H36 Cl2 N7 O P

Formal charge

0

Molecular weight

588.512 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1CCN(CC1)C2CCN(CC2)c3ccc(Nc4ncc(Cl)c(Nc5ccccc5[P](C)(C)=O)n4)cc3Cl
SMILES OpenEye OEToolkits 2.0.7 CN1CCN(CC1)C2CCN(CC2)c3ccc(cc3Cl)Nc4ncc(c(n4)Nc5ccccc5P(=O)(C)C)Cl
Canonical SMILES CACTVS 3.385 CN1CCN(CC1)C2CCN(CC2)c3ccc(Nc4ncc(Cl)c(Nc5ccccc5[P](C)(C)=O)n4)cc3Cl
Canonical SMILES OpenEye OEToolkits 2.0.7 CN1CCN(CC1)C2CCN(CC2)c3ccc(cc3Cl)Nc4ncc(c(n4)Nc5ccccc5P(=O)(C)C)Cl

IUPAC InChI

InChI=1S/C28H36Cl2N7OP/c1-35-14-16-36(17-15-35)21-10-12-37(13-11-21)25-9-8-20(18-22(25)29)32-28-31-19-23(30)27(34-28)33-24-6-4-5-7-26(24)39(2,3)38/h4-9,18-19,21H,10-17H2,1-3H3,(H2,31,32,33,34)

IUPAC InChI key

YVGYDPFKZQBIRJ-UHFFFAOYSA-N
JAU

wwPDB Information

Atom count

75 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-05-09

Last modified at

2022-04-15

Status

Released

Obsoleted

Not Assigned



JAU : Atoms of Molecule

Total Number of Atoms: 75
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C14 C C1 N Y N 0 6.972 2.641 -1.39
2 C11 C C2 N N N 0 8.907 -1.404 -2.062
3 C10 C C3 N N N 0 8.202 -1.796 0.804
4 C13 C C4 N Y N 0 7.501 1.363 -1.434
5 C02 C C5 N Y N 0 3.016 -1.411 1.525
6 C03 C C6 N Y N 0 1.648 -1.318 1.695
7 C05 C C7 N Y N 0 3.663 -0.424 0.775
8 C07 C C8 N Y N 0 5.687 0.57 -0.08
9 C08 C C9 N Y N 0 6.861 0.327 -0.781
10 C15 C C10 N Y N 0 5.804 2.885 -0.693
11 C16 C C11 N Y N 0 5.157 1.853 -0.042
12 C18 C C12 N Y N 0 1.634 0.617 0.442
13 C20 C C13 N Y N 0 -0.485 1.663 -0.046
14 C21 C C14 N Y N 0 -1.167 2.849 0.195
15 C22 C C15 N Y N 0 -2.547 2.851 0.257
16 C24 C C16 N Y N 0 -3.253 1.667 0.079
17 C26 C C17 N N N 0 -5.13 0.787 1.215
18 C27 C C18 N N N 0 -6.648 0.925 1.351
19 C28 C C19 N N N 0 -7.311 0.55 0.022
20 C30 C C20 N N N 0 -7.573 -1.228 -1.601
21 C31 C C21 N N N 0 -7.178 -2.67 -1.928
22 C33 C C22 N N N 0 -7.381 -4.967 -1.188
23 C34 C C23 N N N 0 -7.119 -3.189 0.435
24 C35 C C24 N N N 0 -7.514 -1.747 0.762
25 C36 C C25 N N N 0 -6.759 1.45 -1.087
26 C37 C C26 N N N 0 -5.238 1.297 -1.151
27 C38 C C27 N Y N 0 -2.57 0.482 -0.161
28 C39 C C28 N Y N 0 -1.19 0.481 -0.224
29 N04 N N1 N Y N 0 0.994 -0.303 1.147
30 N06 N N2 N N N 0 5.035 -0.477 0.577
31 N17 N N3 N Y N 0 2.944 0.565 0.255
32 N19 N N4 N N N 0 0.914 1.662 -0.115
33 N25 N N5 N N N 0 -4.651 1.668 0.143
34 N29 N N6 N N N 0 -7.016 -0.854 -0.294
35 N32 N N7 N N N 0 -7.676 -3.563 -0.872
36 O12 O O1 N N N 0 6.496 -2.306 -1.232
37 P09 P P1 N N N 0 7.555 -1.348 -0.84
38 CL1 CL CL1 N N N 0 3.912 -2.72 2.231
39 CL2 CL CL2 N N N 0 -3.4 4.333 0.558
40 H1 H H1 N N N 0 7.476 3.45 -1.898
41 H2 H H2 N N N 0 8.519 -1.136 -3.045
42 H3 H H3 N N N 0 9.686 -0.698 -1.774
43 H4 H H4 N N N 0 9.323 -2.41 -2.098
44 H5 H H5 N N N 0 8.981 -1.09 1.092
45 H6 H H6 N N N 0 7.394 -1.763 1.534
46 H7 H H7 N N N 0 8.618 -2.803 0.768
47 H8 H H8 N N N 0 8.414 1.175 -1.979
48 H9 H H9 N N N 0 1.117 -2.063 2.268
49 H10 H H10 N N N 0 5.396 3.885 -0.657
50 H11 H H11 N N N 0 4.244 2.045 0.502
51 H12 H H12 N N N 0 -0.619 3.769 0.333
52 H13 H H13 N N N 0 -4.655 1.067 2.155
53 H14 H H14 N N N 0 -4.879 -0.246 0.975
54 H18 H H18 N N N 0 -7.18 -0.561 -2.368
55 H15 H H15 N N N 0 -7.006 0.259 2.136
56 H16 H H16 N N N 0 -6.899 1.955 1.604
57 H17 H H17 N N N 0 -8.389 0.687 0.101
58 H19 H H19 N N N 0 -8.66 -1.147 -1.571
59 H20 H H20 N N N 0 -7.614 -2.959 -2.884
60 H21 H H21 N N N 0 -6.092 -2.745 -1.986
61 H22 H H22 N N N 0 -7.819 -5.611 -0.425
62 H23 H H23 N N N 0 -7.805 -5.217 -2.161
63 H24 H H24 N N N 0 -6.302 -5.115 -1.213
64 H25 H H25 N N N 0 -6.032 -3.27 0.404
65 H26 H H26 N N N 0 -7.511 -3.857 1.202
66 H27 H H27 N N N 0 -8.6 -1.672 0.82
67 H31 H H31 N N N 0 -4.986 0.261 -1.38
68 H28 H H28 N N N 0 -7.077 -1.458 1.718
69 H29 H H29 N N N 0 -7.195 1.159 -2.042
70 H30 H H30 N N N 0 -7.012 2.488 -0.872
71 H32 H H32 N N N 0 -4.84 1.948 -1.93
72 H33 H H33 N N N 0 -3.118 -0.438 -0.299
73 H34 H H34 N N N 0 -0.659 -0.441 -0.411
74 H35 H H35 N N N 0 5.542 -1.241 0.895
75 H36 H H36 N N N 0 1.379 2.392 -0.553



JAU : Chemical Bonds

Total Number of Bonds: 79
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C11 P09 C P sing 1.82 N N
2 O12 P09 O P doub 1.48 N N
3 CL1 C02 CL C sing 1.74 N N
4 P09 C10 P C sing 1.82 N N
5 P09 C08 P C sing 1.81 N N
6 C08 C13 C C doub 1.38 N Y
7 C08 C07 C C sing 1.39 N Y
8 N06 C07 N C sing 1.4 N N
9 N06 C05 N C sing 1.39 N N
10 C02 C03 C C doub 1.38 N Y
11 C02 C05 C C sing 1.4 N Y
12 C13 C14 C C sing 1.38 N Y
13 C07 C16 C C doub 1.39 N Y
14 C03 N04 C N sing 1.33 N Y
15 C05 N17 C N doub 1.33 N Y
16 C14 C15 C C doub 1.38 N Y
17 C16 C15 C C sing 1.38 N Y
18 N04 C18 N C doub 1.32 N Y
19 N17 C18 N C sing 1.32 N Y
20 C18 N19 C N sing 1.39 N N
21 N19 C20 N C sing 1.4 N N
22 C39 C20 C C doub 1.39 N Y
23 C39 C38 C C sing 1.38 N Y
24 C20 C21 C C sing 1.39 N Y
25 C38 C24 C C doub 1.39 N Y
26 C21 C22 C C doub 1.38 N Y
27 C24 C22 C C sing 1.39 N Y
28 C24 N25 C N sing 1.4 N N
29 C22 CL2 C CL sing 1.74 N N
30 N25 C26 N C sing 1.47 N N
31 N25 C37 N C sing 1.47 N N
32 C26 C27 C C sing 1.53 N N
33 C37 C36 C C sing 1.53 N N
34 C27 C28 C C sing 1.53 N N
35 C36 C28 C C sing 1.53 N N
36 C28 N29 C N sing 1.47 N N
37 C35 N29 C N sing 1.47 N N
38 C35 C34 C C sing 1.53 N N
39 N29 C30 N C sing 1.47 N N
40 C34 N32 C N sing 1.47 N N
41 C30 C31 C C sing 1.53 N N
42 N32 C33 N C sing 1.47 N N
43 N32 C31 N C sing 1.47 N N
44 C14 H1 C H sing 1.08 N N
45 C11 H2 C H sing 1.09 N N
46 C11 H3 C H sing 1.09 N N
47 C11 H4 C H sing 1.09 N N
48 C10 H5 C H sing 1.09 N N
49 C10 H6 C H sing 1.09 N N
50 C10 H7 C H sing 1.09 N N
51 C13 H8 C H sing 1.08 N N
52 C03 H9 C H sing 1.08 N N
53 C15 H10 C H sing 1.08 N N
54 C16 H11 C H sing 1.08 N N
55 C21 H12 C H sing 1.08 N N
56 C26 H13 C H sing 1.09 N N
57 C26 H14 C H sing 1.09 N N
58 C27 H15 C H sing 1.09 N N
59 C27 H16 C H sing 1.09 N N
60 C28 H17 C H sing 1.09 N N
61 C30 H18 C H sing 1.09 N N
62 C30 H19 C H sing 1.09 N N
63 C31 H20 C H sing 1.09 N N
64 C31 H21 C H sing 1.09 N N
65 C33 H22 C H sing 1.09 N N
66 C33 H23 C H sing 1.09 N N
67 C33 H24 C H sing 1.09 N N
68 C34 H25 C H sing 1.09 N N
69 C34 H26 C H sing 1.09 N N
70 C35 H27 C H sing 1.09 N N
71 C35 H28 C H sing 1.09 N N
72 C36 H29 C H sing 1.09 N N
73 C36 H30 C H sing 1.09 N N
74 C37 H31 C H sing 1.09 N N
75 C37 H32 C H sing 1.09 N N
76 C38 H33 C H sing 1.08 N N
77 C39 H34 C H sing 1.08 N N
78 N06 H35 N H sing 0.97 N N
79 N19 H36 N H sing 0.97 N N



JAU : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JAU 7er2 Open in New Window Bound ligand 1 1