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 N01 N N01 N N N 0 5.259 3.563 0.257
2 C02 C C02 N Y N 0 4.065 2.865 0.15
3 C03 C C03 N Y N 0 4.084 1.473 0.107
4 C04 C C04 N Y N 0 2.892 0.785 0.001
5 C05 C C05 N Y N 0 1.702 1.521 -0.06
6 C06 C C06 N Y N 0 1.763 2.911 -0.011
7 N07 N N07 N Y N 0 2.921 3.531 0.096
8 C08 C C08 N Y N 0 0.396 0.829 -0.175
9 C09 C C09 N Y N 0 -0.787 1.561 -0.241
10 C10 C C10 N Y N 0 -1.991 0.866 -0.349
11 N11 N N11 N Y N 0 -1.969 -0.463 -0.384
12 C12 C C12 N Y N 0 -0.825 -1.127 -0.319
13 N13 N N13 N Y N 0 0.338 -0.502 -0.221
14 N14 N N14 N N N 0 -0.845 -2.51 -0.359
15 C15 C C15 N N N 0 -1.694 -3.056 0.71
16 C16 C C16 N N N 0 -1.736 -4.582 0.593
17 O17 O O17 N N N 0 -0.402 -5.095 0.646
18 C18 C C18 N N N 0 0.452 -4.585 -0.382
19 C19 C C19 N N N 0 0.516 -3.06 -0.274
20 N20 N N20 N N N 0 -3.194 1.551 -0.417
21 C21 C C21 N N N 0 -4.325 0.619 -0.527
22 C22 C C22 N N N 0 -5.625 1.417 -0.66
23 O23 O O23 N N N 0 -5.755 2.297 0.459
24 C24 C C24 N N N 0 -4.67 3.219 0.596
25 C25 C C25 N N N 0 -3.361 2.44 0.742
26 C26 C C26 N N N 0 2.872 -0.721 -0.049
27 F27 F F27 N N N 0 2.288 -1.14 -1.249
28 F28 F F28 N N N 0 4.181 -1.208 0.028
29 F29 F F29 N N N 0 2.127 -1.213 1.029
30 HN01 H HN01 N N N 0 5.253 4.533 0.291
31 HN0A H HN0A N N N 0 6.1 3.082 0.301
32 H03 H H03 N N N 0 5.021 0.938 0.156
33 H06 H H06 N N N 0 0.851 3.488 -0.058
34 H09 H H09 N N N 0 -0.773 2.64 -0.209
35 H15 H H15 N N N 0 -1.283 -2.776 1.68
36 H15A H H15A N N N 0 -2.703 -2.655 0.613
37 H16 H H16 N N N 0 -2.318 -4.994 1.417
38 H16A H H16A N N N 0 -2.196 -4.861 -0.355
39 H18 H H18 N N N 0 1.453 -5.001 -0.262
40 H18A H H18A N N N 0 0.056 -4.866 -1.358
41 H19 H H19 N N N 0 1.12 -2.662 -1.09
42 H19A H H19A N N N 0 0.963 -2.78 0.68
43 H21 H H21 N N N 0 -4.194 -0.012 -1.406
44 H21A H H21A N N N 0 -4.371 -0.005 0.366
45 H22 H H22 N N N 0 -5.602 2.0 -1.581
46 H22A H H22A N N N 0 -6.472 0.731 -0.685
47 H24 H H24 N N N 0 -4.619 3.854 -0.288
48 H24A H H24A N N N 0 -4.827 3.837 1.48
49 H25 H H25 N N N 0 -3.391 1.845 1.655
50 H25A H H25A N N N 0 -2.525 3.138 0.789



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: 3
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
SD5 7r26 Open in New Window Bound ligand 1 1