Chemical Components in the PDB

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YUQ : Summary

Code

YUQ

One-letter code

X

Molecule name

7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylamino)phenyl]-1~{H}-indole-2-carboxylic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylamino)phenyl]-1~{H}-indole-2-carboxylic acid

Formula

C25 H27 F N4 O6 S

Formal charge

0

Molecular weight

530.568 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH](N1C[C]2(C[CH](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc(N[S](C)(=O)=O)c(F)c5
SMILES OpenEye OEToolkits 2.0.7 CC(c1cccc2c1[nH]c(c2c3ccc(c(c3)F)NS(=O)(=O)C)C(=O)O)N4CC5(CC(C5)CN)OC4=O
Canonical SMILES CACTVS 3.385 C[C@H](N1C[C@]2(C[C@@H](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc(N[S](C)(=O)=O)c(F)c5
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@H](c1cccc2c1[nH]c(c2c3ccc(c(c3)F)NS(=O)(=O)C)C(=O)O)N4CC5(CC(C5)CN)OC4=O

IUPAC InChI

InChI=1S/C25H27FN4O6S/c1-13(30-12-25(36-24(30)33)9-14(10-25)11-27)16-4-3-5-17-20(22(23(31)32)28-21(16)17)15-6-7-19(18(26)8-15)29-37(2,34)35/h3-8,13-14,28-29H,9-12,27H2,1-2H3,(H,31,32)/t13-,14-,25-/m0/s1

IUPAC InChI key

ISQDCJWTIUTKFQ-DZWULXIXSA-N
YUQ

wwPDB Information

Atom count

64 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-06-21

Last modified at

2024-07-05

Status

Released

Obsoleted

Not Assigned



YUQ : Atoms of Molecule

Total Number of Atoms: 64
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 -0.876 0.279 0.534
2 C01 C C2 N N N 0 4.094 3.685 1.187
3 C02 C C3 S N N 0 3.431 2.306 1.194
4 C03 C C4 N Y N 0 2.063 2.404 0.569
5 C04 C C5 N Y N 0 1.135 1.381 0.755
6 C06 C C6 N Y N 0 -0.019 -0.479 1.315
7 C07 C C7 N N N 0 -0.335 -1.779 1.909
8 C11 C C8 N Y N 0 -2.263 -0.063 0.155
9 C12 C C9 N Y N 0 -3.253 -0.157 1.134
10 C13 C C10 N Y N 0 -4.546 -0.477 0.778
11 C14 C C11 N Y N 0 -4.865 -0.706 -0.555
12 C17 C C12 N N N 0 -7.258 1.434 -0.37
13 C20 C C13 N Y N 0 -3.88 -0.613 -1.536
14 C22 C C14 N Y N 0 -2.586 -0.288 -1.186
15 C23 C C15 N Y N 0 -0.137 1.492 0.164
16 C24 C C16 N Y N 0 -0.456 2.618 -0.599
17 C25 C C17 N Y N 0 0.47 3.608 -0.768
18 C26 C C18 N Y N 0 1.727 3.504 -0.187
19 C28 C C19 N N N 0 4.842 0.12 0.95
20 C29 C C20 N N N 0 5.584 -0.458 -0.259
21 C30 C C21 N N N 0 7.039 -0.855 -0.014
22 C31 C C22 N N N 0 6.78 -2.05 -0.949
23 C32 C C23 N N N 0 7.422 -3.354 -0.47
24 C34 C C24 N N N 0 5.291 -1.923 -0.577
25 C36 C C25 N N N 0 4.587 1.495 -0.864
26 F21 F F1 N N N 0 -4.193 -0.837 -2.831
27 N05 N N1 N Y N 0 1.183 0.19 1.441
28 N15 N N2 N N N 0 -6.175 -1.029 -0.912
29 N27 N N3 N N N 0 4.251 1.365 0.428
30 N33 N N4 N N N 0 7.221 -4.4 -1.482
31 O08 O O1 N N N 0 0.588 -2.423 2.653
32 O09 O O2 N N N 0 -1.43 -2.278 1.732
33 O18 O O3 N N N 0 -7.205 -0.675 1.264
34 O19 O O4 N N N 0 -8.597 -0.838 -0.774
35 O35 O O5 N N N 0 5.351 0.488 -1.33
36 O37 O O6 N N N 0 4.235 2.433 -1.552
37 S16 S S1 N N N 0 -7.447 -0.35 -0.098
38 H011 H H1 N N N 0 4.188 4.037 0.16
39 H013 H H2 N N N 0 3.484 4.385 1.757
40 H012 H H3 N N N 0 5.084 3.614 1.639
41 H021 H H4 N N N 0 3.336 1.954 2.221
42 H121 H H5 N N N 0 -3.006 0.02 2.171
43 H131 H H6 N N N 0 -5.312 -0.549 1.536
44 H173 H H7 N N N 0 -6.297 1.762 0.028
45 H172 H H8 N N N 0 -7.299 1.645 -1.438
46 H171 H H9 N N N 0 -8.062 1.966 0.137
47 H221 H H10 N N N 0 -1.822 -0.216 -1.946
48 H241 H H11 N N N 0 -1.431 2.705 -1.054
49 H251 H H12 N N N 0 0.222 4.478 -1.358
50 H261 H H13 N N N 0 2.448 4.295 -0.33
51 H282 H H14 N N N 0 4.062 -0.564 1.285
52 H281 H H15 N N N 0 5.537 0.335 1.761
53 H302 H H16 N N N 0 7.761 -0.14 -0.408
54 H301 H H17 N N N 0 7.247 -1.143 1.016
55 H311 H H18 N N N 0 6.987 -1.837 -1.998
56 H321 H H19 N N N 0 8.489 -3.198 -0.316
57 H322 H H20 N N N 0 6.96 -3.662 0.468
58 H342 H H21 N N N 0 5.007 -2.512 0.295
59 H341 H H22 N N N 0 4.616 -2.061 -1.422
60 H051 H H23 N N N 0 1.949 -0.133 1.941
61 H151 H H24 N N N 0 -6.34 -1.652 -1.637
62 H332 H H25 N N N 0 7.636 -5.271 -1.188
63 H1 H H26 N N N 0 6.24 -4.518 -1.69
64 H2 H H28 N N N 0 0.287 -3.273 3.003



YUQ : Chemical Bonds

Total Number of Bonds: 68
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O18 S16 O S doub 1.42 N N
2 O19 S16 O S doub 1.42 N N
3 S16 C17 S C sing 1.81 N N
4 S16 N15 S N sing 1.66 N N
5 N15 C14 N C sing 1.4 N N
6 C14 C13 C C doub 1.39 N Y
7 C14 C20 C C sing 1.39 N Y
8 C13 C12 C C sing 1.38 N Y
9 F21 C20 F C sing 1.35 N N
10 C20 C22 C C doub 1.38 N Y
11 C12 C11 C C doub 1.4 N Y
12 C22 C11 C C sing 1.4 N Y
13 C11 C10 C C sing 1.48 N N
14 O09 C07 O C doub 1.22 N N
15 C07 C06 C C sing 1.46 N N
16 C07 O08 C O sing 1.35 N N
17 C10 C06 C C doub 1.39 N Y
18 C10 C23 C C sing 1.47 N Y
19 C06 N05 C N sing 1.38 N Y
20 C23 C24 C C doub 1.4 N Y
21 C23 C04 C C sing 1.41 N Y
22 C24 C25 C C sing 1.37 N Y
23 N05 C04 N C sing 1.38 N Y
24 C04 C03 C C doub 1.39 N Y
25 C25 C26 C C doub 1.39 N Y
26 O37 C36 O C doub 1.22 N N
27 C03 C26 C C sing 1.38 N Y
28 C03 C02 C C sing 1.51 N N
29 C36 O35 C O sing 1.35 N N
30 C36 N27 C N sing 1.34 N N
31 O35 C29 O C sing 1.45 N N
32 C30 C29 C C sing 1.53 N N
33 C30 C31 C C sing 1.54 N N
34 N27 C02 N C sing 1.46 N N
35 N27 C28 N C sing 1.47 N N
36 C02 C01 C C sing 1.53 N N
37 C29 C28 C C sing 1.53 N N
38 C29 C34 C C sing 1.53 N N
39 C31 C34 C C sing 1.54 N N
40 C31 C32 C C sing 1.53 N N
41 N33 C32 N C sing 1.47 N N
42 C01 H011 C H sing 1.09 N N
43 C01 H013 C H sing 1.09 N N
44 C01 H012 C H sing 1.09 N N
45 C02 H021 C H sing 1.09 N N
46 C12 H121 C H sing 1.08 N N
47 C13 H131 C H sing 1.08 N N
48 C17 H173 C H sing 1.09 N N
49 C17 H172 C H sing 1.09 N N
50 C17 H171 C H sing 1.09 N N
51 C22 H221 C H sing 1.08 N N
52 C24 H241 C H sing 1.08 N N
53 C25 H251 C H sing 1.08 N N
54 C26 H261 C H sing 1.08 N N
55 C28 H282 C H sing 1.09 N N
56 C28 H281 C H sing 1.09 N N
57 C30 H302 C H sing 1.09 N N
58 C30 H301 C H sing 1.09 N N
59 C31 H311 C H sing 1.09 N N
60 C32 H321 C H sing 1.09 N N
61 C32 H322 C H sing 1.09 N N
62 C34 H342 C H sing 1.09 N N
63 C34 H341 C H sing 1.09 N N
64 N05 H051 N H sing 0.97 N N
65 N15 H151 N H sing 0.97 N N
66 N33 H332 N H sing 1.01 N N
67 N33 H1 N H sing 1.01 N N
68 O08 H2 O H sing 0.97 N N



YUQ : Used in PDB Entries

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