Chemical Components in the PDB

pdbe.org/chem
spacer

13L : Summary

Code

13L

One-letter code

X

Molecule name

3-{4-amino-1-[(3R)-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-[(3R)-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-[(3R)-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-/m1/s1

IUPAC InChI key

OQUNLLPGZMGVNR-HSZRJFAPSA-N
13L

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



13L : 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 -8.289 -0.792 0.761
2 C7 C C7 N Y N 0 -6.171 -0.258 -0.942
3 C6 C C6 N Y N 0 -7.031 -1.277 1.059
4 C9 C C9 N Y N 0 2.399 3.843 0.688
5 C13 C C13 N Y N 0 -8.49 -0.043 -0.384
6 C20 C C20 N N N 0 6.057 -0.293 -2.829
7 C21 C C21 N N N 0 4.645 -0.189 -2.249
8 C8 C C8 N Y N 0 -1.132 -0.476 0.315
9 C18 C C18 N N N 0 -3.6 -0.77 0.205
10 C16 C C16 N Y N 0 2.792 1.641 0.148
11 C19 C C19 N N N 0 7.972 -0.65 0.115
12 C26 C C26 N N N 0 -9.821 2.012 -0.777
13 C1 C C1 N Y N 0 -0.872 -2.863 1.721
14 C2 C C2 N Y N 0 0.25 -2.115 1.419
15 C3 C C3 N Y N 0 -2.123 -2.426 1.337
16 C5 C C5 N Y N 0 -7.432 0.223 -1.234
17 C10 C C10 N Y N 0 1.493 1.323 0.588
18 C11 C C11 N Y N 0 0.126 -0.918 0.715
19 C12 C C12 N Y N 0 -2.261 -1.231 0.626
20 C14 C C14 N Y N 0 -5.966 -1.012 0.207
21 C15 C C15 N Y N 0 1.332 -0.118 0.392
22 C17 C C17 N Y N 0 0.681 2.355 1.086
23 C22 C C22 N N N 0 6.88 -1.272 -1.986
24 C23 C C23 N N N 0 5.525 -0.622 0.048
25 C24 C C24 R N N 0 4.717 0.349 -0.818
26 C25 C C25 N N N 0 10.427 -0.593 0.459
27 C27 C C27 N N N 0 -10.322 -0.075 -2.055
28 C28 C C28 N N N 0 9.307 -0.878 -0.544
29 C29 C C29 N N N 0 -9.864 0.484 -0.707
30 N30 N N30 N Y N 0 3.197 2.909 0.218
31 N31 N N31 N Y N 0 1.176 3.588 1.116
32 N32 N N32 N Y N 0 2.451 -0.571 -0.122
33 N33 N N33 N Y N 0 3.363 0.478 -0.275
34 N34 N N34 N N N 0 6.834 -0.841 -0.582
35 N35 N N35 N N N 0 -0.601 2.095 1.53
36 N36 N N36 N N N 0 -4.691 -1.502 0.506
37 O37 O O37 N N N 0 -3.718 0.271 -0.414
38 O38 O O38 N N N 0 7.921 -0.294 1.274
39 H1 H H1 N N N 0 -9.119 -1.002 1.42
40 H2 H H2 N N N 0 -5.345 -0.05 -1.606
41 H3 H H3 N N N 0 -6.875 -1.862 1.953
42 H4 H H4 N N N 0 2.761 4.86 0.73
43 H5 H H5 N N N 0 6.003 -0.654 -3.856
44 H6 H H6 N N N 0 6.531 0.689 -2.813
45 H7 H H7 N N N 0 4.05 0.488 -2.862
46 H8 H H8 N N N 0 4.181 -1.175 -2.243
47 H9 H H9 N N N 0 -1.232 0.451 -0.23
48 H10 H H10 N N N 0 -10.815 2.393 -1.01
49 H11 H H11 N N N 0 -9.495 2.411 0.184
50 H12 H H12 N N N 0 -9.122 2.32 -1.554
51 H13 H H13 N N N 0 -0.77 -3.79 2.266
52 H14 H H14 N N N 0 1.227 -2.463 1.723
53 H15 H H15 N N N 0 -2.997 -3.015 1.575
54 H16 H H16 N N N 0 -7.592 0.809 -2.128
55 H17 H H17 N N N 0 6.46 -2.273 -2.074
56 H18 H H18 N N N 0 7.913 -1.275 -2.333
57 H19 H H19 N N N 0 5.664 -0.197 1.042
58 H20 H H20 N N N 0 4.994 -1.571 0.125
59 H21 H H21 N N N 0 5.203 1.325 -0.821
60 H22 H H22 N N N 0 10.36 0.442 0.794
61 H23 H H23 N N N 0 10.326 -1.26 1.315
62 H24 H H24 N N N 0 11.393 -0.758 -0.019
63 H25 H H25 N N N 0 -10.353 -1.164 -2.005
64 H26 H H26 N N N 0 -11.316 0.306 -2.288
65 H27 H H27 N N N 0 -9.623 0.233 -2.832
66 H28 H H28 N N N 0 9.375 -1.913 -0.879
67 H29 H H29 N N N 0 9.408 -0.212 -1.401
68 H30 H H30 N N N 0 -10.563 0.176 0.071
69 H31 H H31 N N N 0 -0.961 1.196 1.475
70 H32 H H32 N N N 0 -1.142 2.812 1.897
71 H33 H H33 N N N 0 -4.592 -2.368 0.93



13L : 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 C27 C29 C C sing 1.5294931 N N
2 C29 C26 C C sing 1.5302068 N N
3 C29 C13 C C sing 1.5066301 N N
4 C4 C13 C C doub 1.3829052 N Y
5 C4 C6 C C sing 1.3807943 N Y
6 C13 C5 C C sing 1.3829751 N Y
7 C6 C14 C C doub 1.3893718 N Y
8 C5 C7 C C doub 1.3808497 N Y
9 C14 C7 C C sing 1.3895115 N Y
10 C14 N36 C N sing 1.3982582 N N
11 N36 C18 N C sing 1.3478523 N N
12 C3 C1 C C doub 1.379647 N Y
13 C3 C12 C C sing 1.397351 N Y
14 C18 C12 C C sing 1.4773906 N N
15 C18 O37 C O doub 1.2168673 N N
16 C1 C2 C C sing 1.3818799 N Y
17 C12 C8 C C doub 1.3933367 N Y
18 C2 C11 C C doub 1.3942026 N Y
19 C8 C11 C C sing 1.3920949 N Y
20 C11 C15 C C sing 1.4828234 N N
21 C25 C28 C C sing 1.5302398 N N
22 C15 N32 C N doub 1.3120846 N Y
23 C15 C10 C C sing 1.4631535 N Y
24 N32 N33 N N sing 1.3984113 N Y
25 C22 N34 C N sing 1.4693853 N N
26 C22 C20 C C sing 1.5318025 N N
27 C23 N34 C N sing 1.4691297 N N
28 C23 C24 C C sing 1.531555 N N
29 N34 C19 N C sing 1.3480853 N N
30 N35 C17 N C sing 1.3813978 N N
31 C28 C19 C C sing 1.5061507 N N
32 C10 C17 C C doub 1.4044117 N Y
33 C10 C16 C C sing 1.4078796 N Y
34 C19 O38 C O doub 1.2135147 N N
35 N33 C24 N C sing 1.4645156 N N
36 N33 C16 N C sing 1.3629156 N Y
37 C20 C21 C C sing 1.5300196 N N
38 C21 C24 C C sing 1.5304865 N N
39 C17 N31 C N sing 1.3289899 N Y
40 C16 N30 C N doub 1.3329475 N Y
41 N31 C9 N C doub 1.3205824 N Y
42 N30 C9 N C sing 1.3153175 N Y
43 C4 H1 C H sing 1.0804077 N N
44 C7 H2 C H sing 1.0800166 N N
45 C6 H3 C H sing 1.0797209 N N
46 C9 H4 C H sing 1.0803226 N N
47 C20 H5 C H sing 1.0899385 N N
48 C20 H6 C H sing 1.0905302 N N
49 C21 H7 C H sing 1.0900105 N N
50 C21 H8 C H sing 1.0897375 N N
51 C8 H9 C H sing 1.0799787 N N
52 C26 H10 C H sing 1.0897183 N N
53 C26 H11 C H sing 1.0904119 N N
54 C26 H12 C H sing 1.0895844 N N
55 C1 H13 C H sing 1.0801657 N N
56 C2 H14 C H sing 1.0807631 N N
57 C3 H15 C H sing 1.0804819 N N
58 C5 H16 C H sing 1.0808479 N N
59 C22 H17 C H sing 1.0891029 N N
60 C22 H18 C H sing 1.089728 N N
61 C23 H19 C H sing 1.0899459 N N
62 C23 H20 C H sing 1.0901793 N N
63 C24 H21 C H sing 1.0903124 N N
64 C25 H22 C H sing 1.0899261 N N
65 C25 H23 C H sing 1.0898743 N N
66 C25 H24 C H sing 1.0903509 N N
67 C27 H25 C H sing 1.090588 N N
68 C27 H26 C H sing 1.0897183 N N
69 C27 H27 C H sing 1.0895844 N N
70 C28 H28 C H sing 1.0899881 N N
71 C28 H29 C H sing 1.0900487 N N
72 C29 H30 C H sing 1.0902977 N N
73 N35 H31 N H sing 0.9699619 N N
74 N35 H32 N H sing 0.9702881 N N
75 N36 H33 N H sing 0.9692951 N N



13L : Used in PDB Entries

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