Chemical Components in the PDB

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W9K : Summary

Code

W9K

One-letter code

X

Molecule name

(5R)-7-(4-hydroxyphenyl)-1,8-dithia-3-azaspiro[4.5]dec-6-ene-2,4-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 (5R)-7-(4-hydroxyphenyl)-1,8-dithia-3-azaspiro[4.5]dec-6-ene-2,4-dione
OpenEye OEToolkits 2.0.7 (5~{R})-7-(4-hydroxyphenyl)-1,8-dithia-3-azaspiro[4.5]dec-6-ene-2,4-dione

Formula

C13 H11 N O3 S2

Formal charge

0

Molecular weight

293.361 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Oc1ccc(cc1)C1=CC2(CCS1)SC(=O)NC2=O
SMILES CACTVS 3.385 Oc1ccc(cc1)C2=C[C]3(CCS2)SC(=O)NC3=O
SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1C2=CC3(CCS2)C(=O)NC(=O)S3)O
Canonical SMILES CACTVS 3.385 Oc1ccc(cc1)C2=C[C@@]3(CCS2)SC(=O)NC3=O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1C2=C[C@]3(CCS2)C(=O)NC(=O)S3)O

IUPAC InChI

InChI=1S/C13H11NO3S2/c15-9-3-1-8(2-4-9)10-7-13(5-6-18-10)11(16)14-12(17)19-13/h1-4,7,15H,5-6H2,(H,14,16,17)/t13-/m1/s1

IUPAC InChI key

VJAVMIFSWYAVBZ-CYBMUJFWSA-N
W9K

wwPDB Information

Atom count

30 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-05-09

Last modified at

2023-06-09

Status

Released

Obsoleted

Not Assigned



W9K : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 R N N 0 1.734 -0.203 -0.281
2 C02 C C2 N N N 0 0.296 0.167 -0.166
3 C04 C C3 N N N 0 2.385 -0.232 1.084
4 C05 C C4 N N N 0 1.962 -1.528 -0.995
5 C11 C C8 N Y N 0 -2.1 -0.071 -0.092
6 C06 C C5 N N N 0 -0.742 -0.639 -0.253
7 C07 C C6 N N N 0 3.7 1.475 0.237
8 C10 C C7 N N N 0 1.196 -2.639 -0.263
9 C15 C C9 N Y N 0 -3.026 -0.699 0.74
10 C16 C C10 N Y N 0 -3.72 1.621 -0.62
11 S12 S S2 N N N 0 -0.578 -2.367 -0.554
12 C17 C C11 N Y N 0 -4.29 -0.167 0.888
13 C18 C C12 N Y N 0 -4.64 0.993 0.209
14 S03 S S1 N N N 0 2.648 1.118 -1.145
15 N08 N N1 N N N 0 3.357 0.652 1.23
16 O09 O O1 N N N 0 2.046 -0.995 1.963
17 O13 O O2 N N N 0 4.576 2.318 0.272
18 C14 C C13 N Y N 0 -2.453 1.098 -0.767
19 H21 H H1 N N N 0 0.08 1.21 0.008
20 O19 O O3 N N N 0 -5.888 1.511 0.353
21 H25 H H5 N N N 0 1.407 -2.592 0.806
22 H22 H H2 N N N 0 1.603 -1.454 -2.022
23 H23 H H3 N N N 0 3.027 -1.761 -0.997
24 H26 H H4 N N N 0 1.491 -3.612 -0.656
25 H28 H H6 N N N 0 -2.755 -1.601 1.268
26 H29 H H7 N N N 0 -3.996 2.523 -1.146
27 H30 H H8 N N N 0 -5.008 -0.653 1.532
28 H24 H H9 N N N 0 3.83 0.704 2.075
29 H27 H H10 N N N 0 -1.736 1.589 -1.408
30 H1 H H11 N N N 0 -6.53 1.174 -0.287



W9K : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 C02 C C sing 1.49 N N
2 C01 S03 C S sing 1.82 N N
3 C01 C04 C C sing 1.51 N N
4 C01 C05 C C sing 1.52 N N
5 C02 C06 C C doub 1.32 N N
6 S03 C07 S C sing 1.77 N N
7 C04 N08 C N sing 1.32 N N
8 C04 O09 C O doub 1.21 N N
9 C05 C10 C C sing 1.54 N N
10 C06 C11 C C sing 1.48 N N
11 C06 S12 C S sing 1.76 N N
12 C07 N08 C N sing 1.33 N N
13 C07 O13 C O doub 1.22 N N
14 C10 S12 C S sing 1.82 N N
15 C11 C14 C C doub 1.4 N Y
16 C11 C15 C C sing 1.39 N Y
17 C14 C16 C C sing 1.38 N Y
18 C15 C17 C C doub 1.38 N Y
19 C16 C18 C C doub 1.39 N Y
20 C17 C18 C C sing 1.39 N Y
21 C18 O19 C O sing 1.36 N N
22 C02 H21 C H sing 1.08 N N
23 C05 H22 C H sing 1.09 N N
24 C05 H23 C H sing 1.09 N N
25 C10 H26 C H sing 1.09 N N
26 C10 H25 C H sing 1.09 N N
27 C15 H28 C H sing 1.08 N N
28 C16 H29 C H sing 1.08 N N
29 C17 H30 C H sing 1.08 N N
30 N08 H24 N H sing 0.97 N N
31 C14 H27 C H sing 1.08 N N
32 O19 H1 O H sing 0.97 N N



W9K : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
W9K 7fys Open in New Window Bound ligand 1 1