Chemical Components in the PDB

pdbe.org/chem
spacer

1JD : Summary

Code

1JD

One-letter code

X

Molecule name

(2S)-2-{[1-(3-chloropyridin-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-methylpyridin-2-yl)-3-(propan-2-yloxy)propanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-2-{[1-(3-chloropyridin-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-methylpyridin-2-yl)-3-(propan-2-yloxy)propanamide
OpenEye OEToolkits 1.7.6 (2S)-2-[1-(3-chloranylpyridin-2-yl)pyrazolo[3,4-d]pyrimidin-4-yl]oxy-N-(5-methylpyridin-2-yl)-3-propan-2-yloxy-propanamide

Formula

C22 H22 Cl N7 O3

Formal charge

0

Molecular weight

467.908 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(Nc1ncc(cc1)C)C(Oc2ncnc3c2cnn3c4ncccc4Cl)COC(C)C
SMILES CACTVS 3.370 CC(C)OC[CH](Oc1ncnc2n(ncc12)c3ncccc3Cl)C(=O)Nc4ccc(C)cn4
SMILES OpenEye OEToolkits 1.7.6 Cc1ccc(nc1)NC(=O)C(COC(C)C)Oc2c3cnn(c3ncn2)c4c(cccn4)Cl
Canonical SMILES CACTVS 3.370 CC(C)OC[C@H](Oc1ncnc2n(ncc12)c3ncccc3Cl)C(=O)Nc4ccc(C)cn4
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1ccc(nc1)NC(=O)[C@H](COC(C)C)Oc2c3cnn(c3ncn2)c4c(cccn4)Cl

IUPAC InChI

InChI=1S/C22H22ClN7O3/c1-13(2)32-11-17(21(31)29-18-7-6-14(3)9-25-18)33-22-15-10-28-30(19(15)26-12-27-22)20-16(23)5-4-8-24-20/h4-10,12-13,17H,11H2,1-3H3,(H,25,29,31)/t17-/m0/s1

IUPAC InChI key

AAGISEXHOPCAHZ-KRWDZBQOSA-N
1JD

wwPDB Information

Atom count

55 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-02-14

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



1JD : Atoms of Molecule

Total Number of Atoms: 55
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 8.563 -3.103 0.693
2 C2 C C2 N Y N 0 7.42 -2.238 0.229
3 C3 C C3 N Y N 0 7.597 -1.344 -0.819
4 C4 C C4 N Y N 0 6.521 -0.569 -1.214
5 C5 C C5 N Y N 0 5.307 -0.709 -0.552
6 N1 N N1 N Y N 0 5.178 -1.572 0.444
7 C6 C C6 N Y N 0 6.184 -2.329 0.838
8 N2 N N2 N N N 0 4.215 0.066 -0.939
9 C7 C C7 N N N 0 3.009 -0.137 -0.373
10 O1 O O1 N N N 0 2.893 -0.929 0.539
11 C8 C C8 S N N 0 1.805 0.62 -0.871
12 C9 C C9 N N N 0 2.043 2.122 -0.706
13 O2 O O2 N N N 0 2.371 2.406 0.656
14 C10 C C10 N N N 0 2.614 3.789 0.919
15 C11 C C11 N N N 0 1.301 4.472 1.311
16 C12 C C12 N N N 0 3.619 3.921 2.065
17 O3 O O3 N N N 0 0.654 0.234 -0.117
18 C13 C C13 N Y N 0 -0.541 0.285 -0.751
19 C14 C C14 N Y N 0 -1.724 -0.071 -0.084
20 C15 C C15 N Y N 0 -2.053 -0.533 1.257
21 N3 N N3 N Y N 0 -3.343 -0.709 1.31
22 N4 N N4 N Y N 0 -3.921 -0.393 0.075
23 C16 C C16 N Y N 0 -2.942 0.0 -0.791
24 N5 N N5 N Y N 0 -2.921 0.4 -2.061
25 C17 C C17 N Y N 0 -1.786 0.723 -2.643
26 N6 N N6 N Y N 0 -0.624 0.677 -2.016
27 C18 C C18 N Y N 0 -5.283 -0.469 -0.224
28 C19 C C19 N Y N 0 -6.182 -0.882 0.755
29 C20 C C20 N Y N 0 -7.53 -0.952 0.445
30 C21 C C21 N Y N 0 -7.933 -0.605 -0.838
31 C22 C C22 N Y N 0 -6.985 -0.205 -1.759
32 N7 N N7 N Y N 0 -5.708 -0.143 -1.434
33 CL1 CL CL1 N N N 0 -5.621 -1.304 2.343
34 H1 H H1 N N N 0 8.561 -4.038 0.132
35 H2 H H2 N N N 0 9.505 -2.581 0.525
36 H3 H H3 N N N 0 8.45 -3.316 1.755
37 H4 H H4 N N N 0 8.552 -1.257 -1.314
38 H5 H H5 N N N 0 6.623 0.137 -2.025
39 H6 H H6 N N N 0 6.04 -3.025 1.651
40 H7 H H7 N N N 0 4.323 0.752 -1.617
41 H8 H H8 N N N 0 1.643 0.392 -1.924
42 H9 H H9 N N N 0 2.866 2.433 -1.35
43 H10 H H10 N N N 0 1.14 2.666 -0.983
44 H11 H H11 N N N 0 3.018 4.264 0.025
45 H12 H H12 N N N 0 0.898 3.997 2.205
46 H13 H H13 N N N 0 1.487 5.527 1.512
47 H14 H H14 N N N 0 0.585 4.378 0.495
48 H15 H H15 N N N 0 4.554 3.435 1.787
49 H16 H H16 N N N 0 3.804 4.976 2.266
50 H17 H H17 N N N 0 3.215 3.446 2.96
51 H18 H H18 N N N 0 -1.354 -0.7 2.063
52 H19 H H19 N N N 0 -1.806 1.044 -3.674
53 H20 H H20 N N N 0 -8.251 -1.269 1.184
54 H21 H H21 N N N 0 -8.976 -0.65 -1.112
55 H22 H H22 N N N 0 -7.294 0.066 -2.758



1JD : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.51 N N
2 C3 C2 C C doub 1.39 N Y
3 C3 C4 C C sing 1.38 N Y
4 C2 C6 C C sing 1.38 N Y
5 C4 C5 C C doub 1.39 N Y
6 C6 N1 C N doub 1.32 N Y
7 O1 C7 O C doub 1.21 N N
8 C5 N1 C N sing 1.32 N Y
9 C5 N2 C N sing 1.39 N N
10 C11 C10 C C sing 1.53 N N
11 C7 N2 C N sing 1.35 N N
12 C7 C8 C C sing 1.51 N N
13 C9 C8 C C sing 1.53 N N
14 C9 O2 C O sing 1.43 N N
15 C10 O2 C O sing 1.43 N N
16 C10 C12 C C sing 1.53 N N
17 CL1 C19 CL C sing 1.74 N N
18 C8 O3 C O sing 1.43 N N
19 C15 N3 C N doub 1.3 N Y
20 C15 C14 C C sing 1.46 N Y
21 O3 C13 O C sing 1.35 N N
22 N3 N4 N N sing 1.4 N Y
23 C14 C13 C C doub 1.4 N Y
24 C14 C16 C C sing 1.41 N Y
25 C13 N6 C N sing 1.33 N Y
26 N4 C16 N C sing 1.36 N Y
27 N4 C18 N C sing 1.4 N N
28 C19 C20 C C doub 1.38 N Y
29 C19 C18 C C sing 1.39 N Y
30 C16 N5 C N doub 1.33 N Y
31 N6 C17 N C doub 1.32 N Y
32 C20 C21 C C sing 1.39 N Y
33 C18 N7 C N doub 1.32 N Y
34 C17 N5 C N sing 1.32 N Y
35 N7 C22 N C sing 1.32 N Y
36 C21 C22 C C doub 1.38 N Y
37 C1 H1 C H sing 1.09 N N
38 C1 H2 C H sing 1.09 N N
39 C1 H3 C H sing 1.09 N N
40 C3 H4 C H sing 1.08 N N
41 C4 H5 C H sing 1.08 N N
42 C6 H6 C H sing 1.08 N N
43 N2 H7 N H sing 0.97 N N
44 C8 H8 C H sing 1.09 N N
45 C9 H9 C H sing 1.09 N N
46 C9 H10 C H sing 1.09 N N
47 C10 H11 C H sing 1.09 N N
48 C11 H12 C H sing 1.09 N N
49 C11 H13 C H sing 1.09 N N
50 C11 H14 C H sing 1.09 N N
51 C12 H15 C H sing 1.09 N N
52 C12 H16 C H sing 1.09 N N
53 C12 H17 C H sing 1.09 N N
54 C15 H18 C H sing 1.08 N N
55 C17 H19 C H sing 1.08 N N
56 C20 H20 C H sing 1.08 N N
57 C21 H21 C H sing 1.08 N N
58 C22 H22 C H sing 1.08 N N



1JD : Used in PDB Entries

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