Chemical Components in the PDB

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59M : Summary

Code

59M

One-letter code

X

Molecule name

4-{4-[5-(fluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine

Systematic names

ProgramVersionName
ACDLabs 12.01 4-{4-[5-(fluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine
OpenEye OEToolkits 1.9.2 4-[4-[5-(fluoranylmethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl]-6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidine

Formula

C15 H14 F4 N6 S2

Formal charge

0

Molecular weight

418.435 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c14c(c(ncn1)N2CCN(CC2)c3sc(nn3)CF)cc(CC(F)(F)F)s4
SMILES CACTVS 3.385 FCc1sc(nn1)N2CCN(CC2)c3ncnc4sc(CC(F)(F)F)cc34
SMILES OpenEye OEToolkits 1.9.2 c1c(sc2c1c(ncn2)N3CCN(CC3)c4nnc(s4)CF)CC(F)(F)F
Canonical SMILES CACTVS 3.385 FCc1sc(nn1)N2CCN(CC2)c3ncnc4sc(CC(F)(F)F)cc34
Canonical SMILES OpenEye OEToolkits 1.9.2 c1c(sc2c1c(ncn2)N3CCN(CC3)c4nnc(s4)CF)CC(F)(F)F

IUPAC InChI

InChI=1S/C15H14F4N6S2/c16-7-11-22-23-14(27-11)25-3-1-24(2-4-25)12-10-5-9(6-15(17,18)19)26-13(10)21-8-20-12/h5,8H,1-4,6-7H2

IUPAC InChI key

CUBGJWXDIQEMAV-UHFFFAOYSA-N
59M

wwPDB Information

Atom count

41 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-08-27

Last modified at

2020-06-27

Status

Released

Obsoleted

Not Assigned



59M : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -2.21 -1.615 -1.394
2 C5 C C2 N Y N 0 -1.821 -1.45 -0.062
3 C6 C C3 N Y N 0 -0.635 -2.102 0.361
4 N1 N N1 N Y N 0 0.043 -2.83 -0.513
5 N3 N N2 N Y N 0 -1.457 -2.371 -2.203
6 FAB F F1 N N N 0 -4.244 2.48 -1.038
7 CBA C C4 N N N 0 -4.426 2.216 0.324
8 FAC F F2 N N N 0 -3.23 2.455 1.009
9 FAD F F3 N N N 0 -5.428 3.05 0.83
10 CAL C C5 N N N 0 -4.837 0.754 0.509
11 CAS C C6 N Y N 0 -3.757 -0.145 -0.036
12 SAR S S1 N Y N 0 -3.691 -0.718 -1.692
13 CAF C C7 N Y N 0 -2.744 -0.604 0.672
14 C2 C C8 N Y N 0 -0.366 -2.955 -1.763
15 NAZ N N3 N N N 0 -0.193 -1.98 1.667
16 CAK C C9 N N N 0 1.048 -2.738 1.875
17 CAI C C10 N N N 0 2.163 -2.131 1.02
18 CAJ C C11 N N N 0 -0.013 -0.568 2.032
19 CAH C C12 N N N 0 1.101 0.039 1.177
20 NAY N N4 N N N 0 2.343 -0.719 1.386
21 CAU C C13 N Y N 0 3.395 -0.153 0.68
22 SAQ S S2 N Y N 0 3.957 1.515 0.808
23 NAP N N5 N Y N 0 4.149 -0.758 -0.191
24 NAO N N6 N Y N 0 5.065 -0.086 -0.74
25 CAT C C14 N Y N 0 5.193 1.155 -0.399
26 CAG C C15 N N N 0 6.219 2.12 -0.933
27 FAA F F4 N N N 0 5.704 2.773 -2.058
28 H1 H H1 N N N 0 -4.979 0.548 1.57
29 H2 H H2 N N N 0 -5.768 0.568 -0.025
30 H3 H H3 N N N 0 -2.608 -0.364 1.716
31 H4 H H4 N N N 0 0.215 -3.557 -2.445
32 H5 H H5 N N N 0 1.33 -2.691 2.927
33 H6 H H6 N N N 0 0.893 -3.777 1.586
34 H7 H H7 N N N 0 3.092 -2.673 1.196
35 H8 H H8 N N N 0 1.893 -2.202 -0.033
36 H9 H H9 N N N 0 -0.943 -0.026 1.857
37 H10 H H10 N N N 0 0.257 -0.497 3.086
38 H11 H H11 N N N 0 0.819 -0.008 0.125
39 H12 H H12 N N N 0 1.256 1.078 1.466
40 H17 H H17 N N N 0 6.462 2.855 -0.166
41 H18 H H18 N N N 0 7.121 1.574 -1.212



59M : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 C5 C C sing 1.4 N Y
2 C4 N3 C N doub 1.34 N Y
3 C4 SAR C S sing 1.76 N Y
4 C5 C6 C C doub 1.42 N Y
5 C5 CAF C C sing 1.45 N Y
6 C6 N1 C N sing 1.32 N Y
7 C6 NAZ C N sing 1.38 N N
8 N1 C2 N C doub 1.32 N Y
9 N3 C2 N C sing 1.31 N Y
10 FAB CBA F C sing 1.4 N N
11 CBA FAC C F sing 1.4 N N
12 CBA FAD C F sing 1.4 N N
13 CBA CAL C C sing 1.53 N N
14 CAL CAS C C sing 1.51 N N
15 CAS SAR C S sing 1.75 N Y
16 CAS CAF C C doub 1.32 N Y
17 NAZ CAK N C sing 1.47 N N
18 NAZ CAJ N C sing 1.47 N N
19 CAK CAI C C sing 1.53 N N
20 CAI NAY C N sing 1.47 N N
21 CAJ CAH C C sing 1.53 N N
22 CAH NAY C N sing 1.47 N N
23 NAY CAU N C sing 1.39 N N
24 CAU SAQ C S sing 1.76 N Y
25 CAU NAP C N doub 1.3 N Y
26 SAQ CAT S C sing 1.76 N Y
27 NAP NAO N N sing 1.26 N Y
28 NAO CAT N C doub 1.29 N Y
29 CAT CAG C C sing 1.51 N N
30 CAG FAA C F sing 1.4 N N
31 CAL H1 C H sing 1.09 N N
32 CAL H2 C H sing 1.09 N N
33 CAF H3 C H sing 1.08 N N
34 C2 H4 C H sing 1.08 N N
35 CAK H5 C H sing 1.09 N N
36 CAK H6 C H sing 1.09 N N
37 CAI H7 C H sing 1.09 N N
38 CAI H8 C H sing 1.09 N N
39 CAJ H9 C H sing 1.09 N N
40 CAJ H10 C H sing 1.09 N N
41 CAH H11 C H sing 1.09 N N
42 CAH H12 C H sing 1.09 N N
43 CAG H17 C H sing 1.09 N N
44 CAG H18 C H sing 1.09 N N



59M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
59M 5dda Open in New Window Bound ligand 1 1