Chemical Components in the PDB

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SD5 : Summary

Code

SD5

One-letter code

X

Molecule name

5-[2,6-di(morpholin-4-yl)pyrimidin-4-yl]-4-(trifluoromethyl)pyridin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 5-[2,6-di(morpholin-4-yl)pyrimidin-4-yl]-4-(trifluoromethyl)pyridin-2-amine
OpenEye OEToolkits 1.7.2 5-(2,6-dimorpholin-4-ylpyrimidin-4-yl)-4-(trifluoromethyl)pyridin-2-amine

Formula

C18 H21 F3 N6 O2

Formal charge

0

Molecular weight

410.394 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 FC(F)(F)c1cc(ncc1c3nc(nc(N2CCOCC2)c3)N4CCOCC4)N
SMILES CACTVS 3.370 Nc1cc(c(cn1)c2cc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F
SMILES OpenEye OEToolkits 1.7.2 c1c(c(cnc1N)c2cc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F
Canonical SMILES CACTVS 3.370 Nc1cc(c(cn1)c2cc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F
Canonical SMILES OpenEye OEToolkits 1.7.2 c1c(c(cnc1N)c2cc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F

IUPAC InChI

InChI=1S/C18H21F3N6O2/c19-18(20,21)13-9-15(22)23-11-12(13)14-10-16(26-1-5-28-6-2-26)25-17(24-14)27-3-7-29-8-4-27/h9-11H,1-8H2,(H2,22,23)

IUPAC InChI key

CWHUFRVAEUJCEF-UHFFFAOYSA-N
SD5

wwPDB Information

Atom count

50 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-06-14

Last modified at

2011-12-30

Status

Released

Obsoleted

Not Assigned



SD5 : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C02 N Y N 0 4.065 2.865 0.15
2 C03 C C03 N Y N 0 4.084 1.473 0.107
3 C04 C C04 N Y N 0 2.892 0.785 0.0010
4 C05 C C05 N Y N 0 1.702 1.521 -0.06
5 C06 C C06 N Y N 0 1.763 2.911 -0.011
6 C08 C C08 N Y N 0 0.396 0.829 -0.175
7 C09 C C09 N Y N 0 -0.787 1.561 -0.241
8 C10 C C10 N Y N 0 -1.991 0.866 -0.349
9 C12 C C12 N Y N 0 -0.825 -1.127 -0.319
10 C15 C C15 N N N 0 -1.694 -3.056 0.71
11 C16 C C16 N N N 0 -1.736 -4.582 0.593
12 C18 C C18 N N N 0 0.452 -4.585 -0.382
13 C19 C C19 N N N 0 0.516 -3.06 -0.274
14 C21 C C21 N N N 0 -4.325 0.619 -0.527
15 C22 C C22 N N N 0 -5.625 1.417 -0.66
16 C24 C C24 N N N 0 -4.67 3.219 0.596
17 C25 C C25 N N N 0 -3.361 2.44 0.742
18 C26 C C26 N N N 0 2.872 -0.721 -0.049
19 F27 F F27 N N N 0 2.288 -1.14 -1.249
20 F28 F F28 N N N 0 4.181 -1.208 0.028
21 F29 F F29 N N N 0 2.127 -1.213 1.029
22 H03 H H03 N N N 0 5.021 0.938 0.156
23 H06 H H06 N N N 0 0.851 3.488 -0.058
24 H09 H H09 N N N 0 -0.773 2.64 -0.209
25 H15 H H15 N N N 0 -1.283 -2.776 1.68
26 H15A H H15A N N N 0 -2.703 -2.655 0.613
27 H16 H H16 N N N 0 -2.318 -4.994 1.417
28 H16A H H16A N N N 0 -2.196 -4.861 -0.355
29 H18 H H18 N N N 0 1.453 -5.001 -0.262
30 H18A H H18A N N N 0 0.056 -4.866 -1.358
31 H19 H H19 N N N 0 1.12 -2.662 -1.09
32 H19A H H19A N N N 0 0.963 -2.78 0.68
33 H21 H H21 N N N 0 -4.194 -0.012 -1.406
34 H21A H H21A N N N 0 -4.371 -0.0050 0.366
35 H22 H H22 N N N 0 -5.602 2.0 -1.581
36 H22A H H22A N N N 0 -6.472 0.731 -0.685
37 H24 H H24 N N N 0 -4.619 3.854 -0.288
38 H24A H H24A N N N 0 -4.827 3.837 1.48
39 H25 H H25 N N N 0 -3.391 1.845 1.655
40 H25A H H25A N N N 0 -2.525 3.138 0.789
41 HN01 H HN01 N N N 0 5.253 4.533 0.291
42 HN0A H HN0A N N N 0 6.1 3.082 0.301
43 N01 N N01 N N N 0 5.259 3.563 0.257
44 N07 N N07 N Y N 0 2.921 3.531 0.096
45 N11 N N11 N Y N 0 -1.969 -0.463 -0.384
46 N13 N N13 N Y N 0 0.338 -0.502 -0.221
47 N14 N N14 N N N 0 -0.845 -2.51 -0.359
48 N20 N N20 N N N 0 -3.194 1.551 -0.417
49 O17 O O17 N N N 0 -0.402 -5.095 0.646
50 O23 O O23 N N N 0 -5.755 2.297 0.459



SD5 : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N01 C02 N C sing 1.39 N N
2 N01 HN01 N H sing 0.97 N N
3 N01 HN0A N H sing 0.97 N N
4 C03 C02 C C doub 1.39 N Y
5 C02 N07 C N sing 1.32 N Y
6 C03 C04 C C sing 1.38 N Y
7 C03 H03 C H sing 1.08 N N
8 C26 C04 C C sing 1.51 N N
9 C04 C05 C C doub 1.4 N Y
10 C05 C08 C C sing 1.48 N N
11 C05 C06 C C sing 1.39 N Y
12 N07 C06 N C doub 1.32 N Y
13 C06 H06 C H sing 1.08 N N
14 C09 C08 C C doub 1.39 N Y
15 C08 N13 C N sing 1.33 N Y
16 C09 C10 C C sing 1.39 N Y
17 C09 H09 C H sing 1.08 N N
18 N20 C10 N C sing 1.39 N N
19 C10 N11 C N doub 1.33 N Y
20 N11 C12 N C sing 1.32 N Y
21 N13 C12 N C doub 1.32 N Y
22 C12 N14 C N sing 1.38 N N
23 N14 C19 N C sing 1.47 N N
24 N14 C15 N C sing 1.47 N N
25 C15 C16 C C sing 1.53 N N
26 C15 H15 C H sing 1.09 N N
27 C15 H15A C H sing 1.09 N N
28 C16 O17 C O sing 1.43 N N
29 C16 H16 C H sing 1.09 N N
30 C16 H16A C H sing 1.09 N N
31 C18 O17 C O sing 1.43 N N
32 C19 C18 C C sing 1.53 N N
33 C18 H18 C H sing 1.09 N N
34 C18 H18A C H sing 1.09 N N
35 C19 H19 C H sing 1.09 N N
36 C19 H19A C H sing 1.09 N N
37 C25 N20 C N sing 1.47 N N
38 N20 C21 N C sing 1.47 N N
39 C21 C22 C C sing 1.53 N N
40 C21 H21 C H sing 1.09 N N
41 C21 H21A C H sing 1.09 N N
42 O23 C22 O C sing 1.43 N N
43 C22 H22 C H sing 1.09 N N
44 C22 H22A C H sing 1.09 N N
45 C24 O23 C O sing 1.43 N N
46 C25 C24 C C sing 1.53 N N
47 C24 H24 C H sing 1.09 N N
48 C24 H24A C H sing 1.09 N N
49 C25 H25 C H sing 1.09 N N
50 C25 H25A C H sing 1.09 N N
51 F27 C26 F C sing 1.4 N N
52 F29 C26 F C sing 1.4 N N
53 C26 F28 C F sing 1.4 N N



SD5 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
SD5 3sd5 Open in New Window Bound ligand 1 1
SD5 5m7e Open in New Window Bound ligand 1 1