Chemical Components in the PDB

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1J9 : Summary

Code

1J9

One-letter code

X

Molecule name

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

Systematic names

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

Formula

C21 H18 Cl2 N6 O4

Formal charge

0

Molecular weight

489.311 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Clc1ccc(nc1)NC(=O)C(Oc2ncnc3c2cnn3c4ccccc4Cl)COCCO
SMILES CACTVS 3.370 OCCOC[CH](Oc1ncnc2n(ncc12)c3ccccc3Cl)C(=O)Nc4ccc(Cl)cn4
SMILES OpenEye OEToolkits 1.7.6 c1ccc(c(c1)n2c3c(cn2)c(ncn3)OC(COCCO)C(=O)Nc4ccc(cn4)Cl)Cl
Canonical SMILES CACTVS 3.370 OCCOC[C@H](Oc1ncnc2n(ncc12)c3ccccc3Cl)C(=O)Nc4ccc(Cl)cn4
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(c(c1)n2c3c(cn2)c(ncn3)O[C@@H](COCCO)C(=O)Nc4ccc(cn4)Cl)Cl

IUPAC InChI

InChI=1S/C21H18Cl2N6O4/c22-13-5-6-18(24-9-13)28-20(31)17(11-32-8-7-30)33-21-14-10-27-29(19(14)25-12-26-21)16-4-2-1-3-15(16)23/h1-6,9-10,12,17,30H,7-8,11H2,(H,24,28,31)/t17-/m0/s1

IUPAC InChI key

KTWRHJPPIZQGRW-KRWDZBQOSA-N
1J9

wwPDB Information

Atom count

51 (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



1J9 : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 7.674 0.125 -1.572
2 C10 C C10 N Y N 0 1.076 -0.403 -0.851
3 C11 C C11 N Y N 0 2.42 -0.965 -2.64
4 C12 C C12 S N N 0 -1.258 -0.779 -1.064
5 C13 C C13 N N N 0 -1.488 -2.269 -0.803
6 C14 C C14 N N N 0 -2.123 -3.822 0.909
7 C15 C C15 N N N 0 -2.536 -3.905 2.38
8 C16 C C16 N N N 0 -2.493 -0.0050 -0.683
9 C17 C C17 N Y N 0 -4.831 0.374 -0.869
10 C18 C C18 N Y N 0 -6.053 0.023 -1.431
11 C19 C C19 N Y N 0 -7.201 0.666 -1.0
12 C2 C C2 N Y N 0 8.508 0.623 -0.588
13 C20 C C20 N Y N 0 -7.085 1.641 -0.018
14 C21 C C21 N Y N 0 -5.838 1.938 0.496
15 C3 C C3 N Y N 0 7.982 1.046 0.619
16 C4 C C4 N Y N 0 6.621 0.97 0.846
17 C5 C C5 N Y N 0 5.781 0.47 -0.141
18 C6 C C6 N Y N 0 6.313 0.047 -1.352
19 C7 C C7 N Y N 0 3.47 -0.083 -0.796
20 C8 C C8 N Y N 0 2.22 0.023 -0.154
21 C9 C C9 N Y N 0 2.457 0.574 1.125
22 CL1 CL CL1 N N N 0 -8.493 2.477 0.557
23 CL2 CL CL2 N N N 0 5.962 1.499 2.362
24 H1 H H1 N N N 0 8.087 -0.2 -2.516
25 H10 H H10 N N N 0 -2.922 -4.222 0.284
26 H11 H H11 N N N 0 -1.214 -4.404 0.753
27 H12 H H12 N N N 0 -2.634 -4.951 2.671
28 H13 H H13 N N N 0 -1.777 -3.426 2.998
29 H14 H H14 N N N 0 -4.112 -3.254 3.472
30 H15 H H15 N N N 0 -3.701 -0.898 -2.028
31 H16 H H16 N N N 0 -6.106 -0.739 -2.193
32 H17 H H17 N N N 0 -8.164 0.415 -1.419
33 H18 H H18 N N N 0 -5.742 2.696 1.26
34 H2 H H2 N N N 0 9.572 0.683 -0.762
35 H3 H H3 N N N 0 8.636 1.434 1.386
36 H4 H H4 N N N 0 5.662 -0.342 -2.122
37 H5 H H5 N N N 0 1.705 0.785 1.87
38 H6 H H6 N N N 0 2.495 -1.364 -3.641
39 H7 H H7 N N N 0 -1.044 -0.625 -2.122
40 H8 H H8 N N N 0 -2.273 -2.637 -1.463
41 H9 H H9 N N N 0 -0.566 -2.818 -0.994
42 N1 N N1 N Y N 0 4.4 0.391 0.085
43 N2 N N2 N Y N 0 3.737 0.78 1.256
44 N3 N N3 N Y N 0 1.226 -0.884 -2.078
45 N4 N N4 N Y N 0 3.519 -0.58 -2.03
46 N5 N N5 N N N 0 -3.667 -0.266 -1.293
47 N6 N N6 N Y N 0 -4.762 1.305 0.069
48 O1 O O1 N N N 0 -0.151 -0.324 -0.283
49 O2 O O2 N N N 0 -1.882 -2.458 0.558
50 O3 O O3 N N N 0 -3.788 -3.241 2.561
51 O4 O O4 N N N 0 -2.432 0.851 0.173



1J9 : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C6 C C doub 1.380871 N Y
2 C1 C2 C C sing 1.3826844 N Y
3 C6 C5 C C sing 1.3886951 N Y
4 C2 C3 C C doub 1.382915 N Y
5 N4 C11 N C doub 1.3145821 N Y
6 N4 C7 N C sing 1.3312273 N Y
7 C11 N3 C N sing 1.322135 N Y
8 C5 N1 C N sing 1.4015983 N N
9 C5 C4 C C doub 1.3891612 N Y
10 N3 C10 N C doub 1.32642 N Y
11 C7 N1 C N sing 1.3659198 N Y
12 C7 C8 C C doub 1.4092196 N Y
13 C3 C4 C C sing 1.3818922 N Y
14 O3 C15 O C sing 1.4286921 N N
15 N1 N2 N N sing 1.4007609 N Y
16 C4 CL2 C CL sing 1.7356204 N N
17 C10 C8 C C sing 1.4057101 N Y
18 C10 O1 C O sing 1.354398 N N
19 C8 C9 C C sing 1.412661 N Y
20 C15 C14 C C sing 1.5301304 N N
21 N2 C9 N C doub 1.3030721 N Y
22 O2 C14 O C sing 1.428908 N N
23 O2 C13 O C sing 1.4294327 N N
24 C12 O1 C O sing 1.4291378 N N
25 C12 C13 C C sing 1.5300722 N N
26 C12 C16 C C sing 1.5064734 N N
27 N5 C16 N C sing 1.3485166 N N
28 N5 C17 N C sing 1.3943715 N N
29 C16 O4 C O doub 1.2121028 N N
30 N6 C17 N C doub 1.3233918 N Y
31 N6 C21 N C sing 1.3193915 N Y
32 C17 C18 C C sing 1.3900824 N Y
33 C21 C20 C C doub 1.3810916 N Y
34 C18 C19 C C doub 1.3845989 N Y
35 C20 C19 C C sing 1.3886702 N Y
36 C20 CL1 C CL sing 1.7355071 N N
37 C1 H1 C H sing 1.0804305 N N
38 C2 H2 C H sing 1.0798018 N N
39 C3 H3 C H sing 1.080069 N N
40 C6 H4 C H sing 1.0807507 N N
41 C9 H5 C H sing 1.0793748 N N
42 C11 H6 C H sing 1.0801977 N N
43 C12 H7 C H sing 1.0903559 N N
44 C13 H8 C H sing 1.0896095 N N
45 C13 H9 C H sing 1.0899385 N N
46 C14 H10 C H sing 1.0904247 N N
47 C14 H11 C H sing 1.0905691 N N
48 C15 H12 C H sing 1.0901381 N N
49 C15 H13 C H sing 1.0897 N N
50 O3 H14 O H sing 0.9669881 N N
51 N5 H15 N H sing 0.96995103 N N
52 C18 H16 C H sing 1.0789332 N N
53 C19 H17 C H sing 1.0797828 N N
54 C21 H18 C H sing 1.080498 N N



1J9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1J9 4iwv Open in New Window Bound ligand 1 1