Chemical Components in the PDB

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W3W : Summary

Code

W3W

One-letter code

X

Molecule name

5-[3,5-bis(fluoranyl)phenyl]-1-[(1S)-1-[3-(1H-imidazol-5-yl)phenyl]ethyl]pyrimidine-2,4-dione

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 5-[3,5-bis(fluoranyl)phenyl]-1-[(1~{S})-1-[3-(1~{H}-imidazol-5-yl)phenyl]ethyl]pyrimidine-2,4-dione

Formula

C21 H16 F2 N4 O2

Formal charge

0

Molecular weight

394.374 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH](N1C=C(C(=O)NC1=O)c2cc(F)cc(F)c2)c3cccc(c3)c4[nH]cnc4
SMILES OpenEye OEToolkits 2.0.7 CC(c1cccc(c1)c2cnc[nH]2)N3C=C(C(=O)NC3=O)c4cc(cc(c4)F)F
Canonical SMILES CACTVS 3.385 C[C@H](N1C=C(C(=O)NC1=O)c2cc(F)cc(F)c2)c3cccc(c3)c4[nH]cnc4
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@H](c1cccc(c1)c2cnc[nH]2)N3C=C(C(=O)NC3=O)c4cc(cc(c4)F)F

IUPAC InChI

InChI=1S/C21H16F2N4O2/c1-12(13-3-2-4-14(5-13)19-9-24-11-25-19)27-10-18(20(28)26-21(27)29)15-6-16(22)8-17(23)7-15/h2-12H,1H3,(H,24,25)(H,26,28,29)/t12-/m0/s1

IUPAC InChI key

BZAXKVPYXQKLNZ-LBPRGKRZSA-N
W3W

wwPDB Information

Atom count

45 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-04-26

Last modified at

2023-06-30

Status

Released

Obsoleted

Not Assigned



W3W : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 1.295 -2.647 -0.868
2 C2 C C2 N Y N 0 2.209 -1.493 -1.188
3 C3 C C3 N Y N 0 2.798 -1.403 -2.436
4 C7 C C4 N Y N 0 2.453 -0.524 -0.236
5 C8 C C5 N Y N 0 3.565 1.587 0.482
6 C9 C C6 N Y N 0 3.065 1.638 1.746
7 C10 C C7 N Y N 0 4.333 3.369 1.504
8 C11 C C8 N N N 0 -0.649 -1.244 -0.397
9 C12 C C9 N N N 0 -1.639 -0.82 0.439
10 C13 C C10 N N N 0 -1.713 -1.405 1.784
11 C14 C C11 N N N 0 0.146 -2.722 1.265
12 C15 C C12 N Y N 0 -2.615 0.207 0.001
13 C16 C C13 N Y N 0 -2.187 1.502 -0.285
14 C19 C C14 N Y N 0 -4.87 0.838 -0.539
15 C20 C C15 N Y N 0 -3.963 -0.122 -0.13
16 N N N1 N Y N 0 3.554 2.734 2.338
17 C C C16 N N N 0 0.674 -3.179 -2.162
18 O O O1 N N N 0 -2.58 -1.057 2.565
19 N1 N N2 N Y N 0 4.372 2.693 0.336
20 O1 O O2 N N N 0 0.956 -3.562 1.606
21 N2 N N3 N N N 0 0.233 -2.194 0.033
22 N3 N N4 N N N 0 -0.802 -2.335 2.137
23 C4 C C17 N Y N 0 3.639 -0.346 -2.738
24 C5 C C18 N Y N 0 3.895 0.626 -1.793
25 C6 C C19 N Y N 0 3.299 0.545 -0.534
26 C17 C C20 N Y N 0 -3.101 2.455 -0.693
27 C18 C C21 N Y N 0 -4.441 2.125 -0.817
28 F F F1 N N N 0 -6.177 0.521 -0.667
29 F1 F F2 N N N 0 -2.687 3.711 -0.971
30 H1 H H1 N N N 0 1.867 -3.441 -0.387
31 H2 H H2 N N N 0 2.601 -2.162 -3.179
32 H3 H H3 N N N 0 1.989 -0.592 0.737
33 H4 H H4 N N N 0 2.393 0.921 2.193
34 H5 H H5 N N N 0 4.862 4.287 1.715
35 H6 H H6 N N N 0 -0.565 -0.835 -1.393
36 H7 H H7 N N N 0 -1.143 1.76 -0.189
37 H8 H H8 N N N 0 -4.299 -1.125 0.086
38 H10 H H10 N N N 0 0.103 -2.385 -2.644
39 H11 H H11 N N N 0 1.465 -3.516 -2.832
40 H12 H H12 N N N 0 0.013 -4.014 -1.931
41 H13 H H13 N N N 0 4.873 2.94 -0.457
42 H14 H H14 N N N 0 -0.837 -2.736 3.02
43 H15 H H15 N N N 0 4.096 -0.283 -3.714
44 H16 H H16 N N N 0 4.551 1.451 -2.03
45 H17 H H17 N N N 0 -5.152 2.873 -1.136



W3W : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C C1 C C sing 1.53 N N
2 F1 C17 F C sing 1.35 N N
3 C1 N2 C N sing 1.46 N N
4 C1 C2 C C sing 1.51 N N
5 C16 C17 C C doub 1.38 N Y
6 C16 C15 C C sing 1.39 N Y
7 C17 C18 C C sing 1.39 N Y
8 N2 C11 N C sing 1.37 N N
9 N2 C14 N C sing 1.34 N N
10 C11 C12 C C doub 1.36 N N
11 O1 C14 O C doub 1.22 N N
12 C14 N3 C N sing 1.34 N N
13 C12 C15 C C sing 1.48 N N
14 C12 C13 C C sing 1.47 N N
15 C3 C2 C C doub 1.38 N Y
16 C3 C4 C C sing 1.38 N Y
17 N3 C13 N C sing 1.35 N N
18 C15 C20 C C doub 1.39 N Y
19 C2 C7 C C sing 1.38 N Y
20 C13 O C O doub 1.22 N N
21 C18 C19 C C doub 1.38 N Y
22 C4 C5 C C doub 1.38 N Y
23 C20 C19 C C sing 1.38 N Y
24 C19 F C F sing 1.35 N N
25 C7 C6 C C doub 1.4 N Y
26 C5 C6 C C sing 1.4 N Y
27 C6 C8 C C sing 1.48 N N
28 C8 N1 C N sing 1.38 N Y
29 C8 C9 C C doub 1.36 N Y
30 N1 C10 N C sing 1.35 N Y
31 C9 N C N sing 1.34 N Y
32 C10 N C N doub 1.31 N Y
33 C1 H1 C H sing 1.09 N N
34 C3 H2 C H sing 1.08 N N
35 C7 H3 C H sing 1.08 N N
36 C9 H4 C H sing 1.08 N N
37 C10 H5 C H sing 1.08 N N
38 C11 H6 C H sing 1.08 N N
39 C16 H7 C H sing 1.08 N N
40 C20 H8 C H sing 1.08 N N
41 C H10 C H sing 1.09 N N
42 C H11 C H sing 1.09 N N
43 C H12 C H sing 1.09 N N
44 N1 H13 N H sing 0.97 N N
45 N3 H14 N H sing 0.97 N N
46 C4 H15 C H sing 1.08 N N
47 C5 H16 C H sing 1.08 N N
48 C18 H17 C H sing 1.08 N N



W3W : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
W3W 8ov7 Open in New Window Bound ligand 1 1