Chemical Components in the PDB

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13J : Summary

Code

13J

One-letter code

X

Molecule name

3-{4-amino-1-[(3S)-1-propanoylpiperidin-3-yl]-1H-pyrazolo[3,4-d]pyrimidin-3-yl}-N-[4-(propan-2-yl)phenyl]benzamide

Systematic names

ProgramVersionName
ACDLabs 12.01 3-{4-amino-1-[(3S)-1-propanoylpiperidin-3-yl]-1H-pyrazolo[3,4-d]pyrimidin-3-yl}-N-[4-(propan-2-yl)phenyl]benzamide
OpenEye OEToolkits 1.7.6 3-[4-azanyl-1-[(3S)-1-propanoylpiperidin-3-yl]pyrazolo[3,4-d]pyrimidin-3-yl]-N-(4-propan-2-ylphenyl)benzamide

Formula

C29 H33 N7 O2

Formal charge

0

Molecular weight

511.618 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(Nc1ccc(cc1)C(C)C)c5cccc(c3nn(c2ncnc(c23)N)C4CCCN(C(=O)CC)C4)c5
SMILES CACTVS 3.370 CCC(=O)N1CCC[CH](C1)n2nc(c3cccc(c3)C(=O)Nc4ccc(cc4)C(C)C)c5c(N)ncnc25
SMILES OpenEye OEToolkits 1.7.6 CCC(=O)N1CCCC(C1)n2c3c(c(n2)c4cccc(c4)C(=O)Nc5ccc(cc5)C(C)C)c(ncn3)N
Canonical SMILES CACTVS 3.370 CCC(=O)N1CCC[C@@H](C1)n2nc(c3cccc(c3)C(=O)Nc4ccc(cc4)C(C)C)c5c(N)ncnc25
Canonical SMILES OpenEye OEToolkits 1.7.6 CCC(=O)N1CCC[C@@H](C1)n2c3c(c(n2)c4cccc(c4)C(=O)Nc5ccc(cc5)C(C)C)c(ncn3)N

IUPAC InChI

InChI=1S/C29H33N7O2/c1-4-24(37)35-14-6-9-23(16-35)36-28-25(27(30)31-17-32-28)26(34-36)20-7-5-8-21(15-20)29(38)33-22-12-10-19(11-13-22)18(2)3/h5,7-8,10-13,15,17-18,23H,4,6,9,14,16H2,1-3H3,(H,33,38)(H2,30,31,32)/t23-/m0/s1

IUPAC InChI key

OQUNLLPGZMGVNR-QHCPKHFHSA-N
13J

wwPDB Information

Atom count

71 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-10-03

Last modified at

2012-11-09

Status

Released

Obsoleted

Not Assigned



13J : Atoms of Molecule

Total Number of Atoms: 71
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C4 N Y N 0 -6.587 2.191 -0.048
2 C7 C C7 N Y N 0 -6.992 -0.529 0.273
3 C6 C C6 N Y N 0 -5.521 1.372 0.266
4 C9 C C9 N Y N 0 4.615 -3.738 -1.36
5 C13 C C13 N Y N 0 -7.852 1.655 -0.201
6 C20 C C20 N N N 0 4.536 2.779 -2.057
7 C21 C C21 N N N 0 3.571 1.627 -1.768
8 C8 C C8 N Y N 0 -0.979 -1.07 0.209
9 C18 C C18 N N N 0 -3.411 -0.547 0.268
10 C16 C C16 N Y N 0 3.582 -1.772 -0.758
11 C19 C C19 N N N 0 6.462 2.809 0.901
12 C26 C C26 N N N 0 -9.626 2.109 -1.874
13 C1 C C1 N Y N 0 -1.351 -3.181 1.984
14 C2 C C2 N Y N 0 -0.086 -2.896 1.507
15 C3 C C3 N Y N 0 -2.431 -2.416 1.592
16 C5 C C5 N Y N 0 -8.054 0.296 -0.04
17 C10 C C10 N Y N 0 2.445 -2.509 -0.378
18 C11 C C11 N Y N 0 0.107 -1.84 0.617
19 C12 C C12 N Y N 0 -2.252 -1.358 0.697
20 C14 C C14 N Y N 0 -5.719 0.0060 0.423
21 C15 C C15 N Y N 0 1.465 -1.537 0.106
22 C17 C C17 N Y N 0 2.468 -3.905 -0.529
23 C22 C C22 N N N 0 4.818 3.542 -0.759
24 C23 C C23 N N N 0 4.492 1.398 0.542
25 C24 C C24 S N N 0 4.213 0.66 -0.771
26 C25 C C25 N N N 0 8.538 4.043 1.461
27 C27 C C27 N N N 0 -10.07 2.462 0.56
28 C28 C C28 N N N 0 7.279 4.037 0.592
29 C29 C C29 N N N 0 -9.013 2.552 -0.543
30 N30 N N30 N Y N 0 4.637 -2.429 -1.241
31 N31 N N31 N Y N 0 3.568 -4.468 -1.02
32 N32 N N32 N Y N 0 2.01 -0.348 0.0060
33 N33 N N33 N Y N 0 3.303 -0.46 -0.519
34 N34 N N34 N N N 0 5.301 2.592 0.252
35 N35 N N35 N N N 0 1.378 -4.674 -0.171
36 N36 N N36 N N N 0 -4.642 -0.827 0.741
37 O37 O O37 N N N 0 -3.254 0.373 -0.511
38 O38 O O38 N N N 0 6.849 2.017 1.734
39 H1 H H1 N N N 0 -6.433 3.253 -0.17
40 H2 H H2 N N N 0 -7.15 -1.591 0.395
41 H3 H H3 N N N 0 -4.533 1.792 0.389
42 H4 H H4 N N N 0 5.488 -4.237 -1.756
43 H5 H H5 N N N 0 5.469 2.381 -2.456
44 H6 H H6 N N N 0 4.087 3.454 -2.786
45 H7 H H7 N N N 0 2.648 2.023 -1.347
46 H8 H H8 N N N 0 3.349 1.097 -2.695
47 H9 H H9 N N N 0 -0.835 -0.251 -0.48
48 H10 H H10 N N N 0 -10.466 2.758 -2.121
49 H11 H H11 N N N 0 -8.873 2.173 -2.659
50 H12 H H12 N N N 0 -9.975 1.08 -1.788
51 H13 H H13 N N N 0 -1.494 -4.0 2.672
52 H14 H H14 N N N 0 0.755 -3.499 1.818
53 H15 H H15 N N N 0 -3.417 -2.643 1.968
54 H16 H H16 N N N 0 -9.043 -0.12 -0.161
55 H17 H H17 N N N 0 5.579 4.301 -0.94
56 H18 H H18 N N N 0 3.903 4.018 -0.409
57 H19 H H19 N N N 0 3.55 1.697 1.0
58 H20 H H20 N N N 0 5.039 0.743 1.221
59 H21 H H21 N N N 0 5.15 0.282 -1.182
60 H22 H H22 N N N 0 8.254 4.051 2.513
61 H23 H H23 N N N 0 9.129 3.152 1.25
62 H24 H H24 N N N 0 9.129 4.931 1.238
63 H25 H H25 N N N 0 -9.633 2.778 1.507
64 H26 H H26 N N N 0 -10.91 3.111 0.312
65 H27 H H27 N N N 0 -10.419 1.433 0.645
66 H28 H H28 N N N 0 7.563 4.03 -0.46
67 H29 H H29 N N N 0 6.688 4.929 0.803
68 H30 H H30 N N N 0 -8.664 3.581 -0.629
69 H31 H H31 N N N 0 0.513 -4.256 -0.035
70 H32 H H32 N N N 0 1.477 -5.632 -0.056
71 H33 H H33 N N N 0 -4.78 -1.606 1.302



13J : Chemical Bonds

Total Number of Bonds: 75
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C26 C29 C C sing 1.53 N N
2 C29 C27 C C sing 1.53 N N
3 C29 C13 C C sing 1.51 N N
4 C5 C13 C C doub 1.38 N Y
5 C5 C7 C C sing 1.38 N Y
6 C13 C4 C C sing 1.38 N Y
7 C7 C14 C C doub 1.39 N Y
8 C4 C6 C C doub 1.38 N Y
9 C14 C6 C C sing 1.39 N Y
10 C14 N36 C N sing 1.4 N N
11 N36 C18 N C sing 1.35 N N
12 C3 C1 C C doub 1.38 N Y
13 C3 C12 C C sing 1.4 N Y
14 C18 C12 C C sing 1.48 N N
15 C18 O37 C O doub 1.22 N N
16 C1 C2 C C sing 1.38 N Y
17 C25 C28 C C sing 1.53 N N
18 C12 C8 C C doub 1.39 N Y
19 C28 C19 C C sing 1.51 N N
20 C2 C11 C C doub 1.39 N Y
21 C8 C11 C C sing 1.39 N Y
22 C11 C15 C C sing 1.48 N N
23 C19 O38 C O doub 1.21 N N
24 C19 N34 C N sing 1.35 N N
25 N32 C15 N C doub 1.31 N Y
26 N32 N33 N N sing 1.4 N Y
27 C15 C10 C C sing 1.46 N Y
28 C23 N34 C N sing 1.47 N N
29 C23 C24 C C sing 1.53 N N
30 N34 C22 N C sing 1.47 N N
31 N33 C24 N C sing 1.46 N N
32 N33 C16 N C sing 1.36 N Y
33 C24 C21 C C sing 1.53 N N
34 C10 C16 C C doub 1.41 N Y
35 C10 C17 C C sing 1.4 N Y
36 N35 C17 N C sing 1.38 N N
37 C16 N30 C N sing 1.33 N Y
38 C17 N31 C N doub 1.33 N Y
39 C22 C20 C C sing 1.53 N N
40 C21 C20 C C sing 1.53 N N
41 N30 C9 N C doub 1.31 N Y
42 N31 C9 N C sing 1.32 N Y
43 C4 H1 C H sing 1.08 N N
44 C7 H2 C H sing 1.08 N N
45 C6 H3 C H sing 1.08 N N
46 C9 H4 C H sing 1.08 N N
47 C20 H5 C H sing 1.09 N N
48 C20 H6 C H sing 1.09 N N
49 C21 H7 C H sing 1.09 N N
50 C21 H8 C H sing 1.09 N N
51 C8 H9 C H sing 1.08 N N
52 C26 H10 C H sing 1.09 N N
53 C26 H11 C H sing 1.09 N N
54 C26 H12 C H sing 1.09 N N
55 C1 H13 C H sing 1.08 N N
56 C2 H14 C H sing 1.08 N N
57 C3 H15 C H sing 1.08 N N
58 C5 H16 C H sing 1.08 N N
59 C22 H17 C H sing 1.09 N N
60 C22 H18 C H sing 1.09 N N
61 C23 H19 C H sing 1.09 N N
62 C23 H20 C H sing 1.09 N N
63 C24 H21 C H sing 1.09 N N
64 C25 H22 C H sing 1.09 N N
65 C25 H23 C H sing 1.09 N N
66 C25 H24 C H sing 1.09 N N
67 C27 H25 C H sing 1.09 N N
68 C27 H26 C H sing 1.09 N N
69 C27 H27 C H sing 1.09 N N
70 C28 H28 C H sing 1.09 N N
71 C28 H29 C H sing 1.09 N N
72 C29 H30 C H sing 1.09 N N
73 N35 H31 N H sing 0.97 N N
74 N35 H32 N H sing 0.97 N N
75 N36 H33 N H sing 0.97 N N



13J : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
13J 4hcv Open in New Window Bound ligand 1 1