Chemical Components in the PDB

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H7S : Summary

Code

H7S

One-letter code

X

Molecule name

(3S)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione
OpenEye OEToolkits 2.0.6 (3~{S})-3-(5-fluoranyl-1~{H}-indol-3-yl)pyrrolidine-2,5-dione

Formula

C12 H9 F N2 O2

Formal charge

0

Molecular weight

232.21 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1(C(NC(=O)C1)=O)c2cnc3c2cc(cc3)F
SMILES CACTVS 3.385 Fc1ccc2[nH]cc([CH]3CC(=O)NC3=O)c2c1
SMILES OpenEye OEToolkits 2.0.6 c1cc2c(cc1F)c(c[nH]2)C3CC(=O)NC3=O
Canonical SMILES CACTVS 3.385 Fc1ccc2[nH]cc([C@@H]3CC(=O)NC3=O)c2c1
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cc2c(cc1F)c(c[nH]2)[C@@H]3CC(=O)NC3=O

IUPAC InChI

InChI=1S/C12H9FN2O2/c13-6-1-2-10-7(3-6)9(5-14-10)8-4-11(16)15-12(8)17/h1-3,5,8,14H,4H2,(H,15,16,17)/t8-/m0/s1

IUPAC InChI key

MXKLDYKORJEOPR-QMMMGPOBSA-N
H7S

wwPDB Information

Atom count

26 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-06-13

Last modified at

2019-12-27

Status

Released

Obsoleted

Not Assigned



H7S : Atoms of Molecule

Total Number of Atoms: 26
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 1.332 0.679 -0.208
2 C2 C C2 N N N 0 2.229 0.712 1.01
3 C4 C C3 N N N 0 3.628 0.147 -0.662
4 C5 C C4 N N N 0 2.29 0.292 -1.353
5 CG C C5 N Y N 0 0.253 -0.361 -0.044
6 CD1 C C6 N Y N 0 0.436 -1.674 0.163
7 NE1 N N1 N Y N 0 -0.775 -2.303 0.263
8 CE2 C C7 N Y N 0 -1.793 -1.386 0.118
9 CD2 C C8 N Y N 0 -1.193 -0.129 -0.075
10 CE3 C C9 N Y N 0 -1.99 1.005 -0.252
11 CZ3 C C10 N Y N 0 -3.362 0.882 -0.235
12 CH2 C C11 N Y N 0 -3.953 -0.361 -0.044
13 CZ2 C C12 N Y N 0 -3.18 -1.487 0.135
14 N3 N N2 N N N 0 3.479 0.402 0.644
15 O6 O O1 N N N 0 4.67 -0.153 -1.204
16 O7 O O2 N N N 0 1.873 0.978 2.137
17 F8 F F1 N N N 0 -4.136 1.976 -0.406
18 H1 H H1 N N N 0 0.895 1.661 -0.389
19 H2 H H2 N N N 0 1.986 -0.653 -1.804
20 H3 H H3 N N N 0 2.329 1.081 -2.104
21 H4 H H4 N N N 0 1.396 -2.162 0.239
22 H5 H H5 N N N 0 -0.898 -3.254 0.412
23 H6 H H6 N N N 0 -1.533 1.972 -0.4
24 H7 H H7 N N N 0 -5.03 -0.445 -0.03
25 H8 H H8 N N N 0 -3.65 -2.447 0.283
26 H9 H H9 N N N 0 4.216 0.365 1.273



H7S : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CH2 CZ2 C C doub 1.38 N Y
2 CH2 CZ3 C C sing 1.39 N Y
3 CZ2 CE2 C C sing 1.39 N Y
4 F8 CZ3 F C sing 1.35 N N
5 CZ3 CE3 C C doub 1.38 N Y
6 CE2 NE1 C N sing 1.38 N Y
7 CE2 CD2 C C doub 1.41 N Y
8 CE3 CD2 C C sing 1.4 N Y
9 NE1 CD1 N C sing 1.37 N Y
10 CD2 CG C C sing 1.46 N Y
11 CD1 CG C C doub 1.34 N Y
12 CG C1 C C sing 1.51 N N
13 O7 C2 O C doub 1.21 N N
14 C1 C2 C C sing 1.51 N N
15 C1 C5 C C sing 1.54 N N
16 C2 N3 C N sing 1.34 N N
17 C5 C4 C C sing 1.51 N N
18 N3 C4 N C sing 1.34 N N
19 C4 O6 C O doub 1.21 N N
20 C1 H1 C H sing 1.09 N N
21 C5 H2 C H sing 1.09 N N
22 C5 H3 C H sing 1.09 N N
23 CD1 H4 C H sing 1.08 N N
24 NE1 H5 N H sing 0.97 N N
25 CE3 H6 C H sing 1.08 N N
26 CH2 H7 C H sing 1.08 N N
27 CZ2 H8 C H sing 1.08 N N
28 N3 H9 N H sing 0.97 N N



H7S : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
H7S 6pyy Open in New Window Bound ligand 8 1
H7S 6pyz Open in New Window Bound ligand 4 1