Chemical Components in the PDB

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D4Y : Summary

Code

D4Y

One-letter code

X

Molecule name

(3S)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one
OpenEye OEToolkits 2.0.6 (3~{S})-5-fluoranyl-3-oxidanyl-1,3-dihydroindol-2-one

Formula

C8 H6 F N O2

Formal charge

0

Molecular weight

167.137 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c12C(C(=O)Nc1ccc(c2)F)O
SMILES CACTVS 3.385 O[CH]1C(=O)Nc2ccc(F)cc12
SMILES OpenEye OEToolkits 2.0.6 c1cc2c(cc1F)C(C(=O)N2)O
Canonical SMILES CACTVS 3.385 O[C@@H]1C(=O)Nc2ccc(F)cc12
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cc2c(cc1F)[C@@H](C(=O)N2)O

IUPAC InChI

InChI=1S/C8H6FNO2/c9-4-1-2-6-5(3-4)7(11)8(12)10-6/h1-3,7,11H,(H,10,12)/t7-/m0/s1

IUPAC InChI key

XYDTZHMQTYEJQN-ZETCQYMHSA-N
D4Y

wwPDB Information

Atom count

18 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-10-18

Last modified at

2018-09-07

Status

Released

Obsoleted

Not Assigned



D4Y : Atoms of Molecule

Total Number of Atoms: 18
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C7 C C1 N Y N 0 -0.008 -0.382 0.187
2 C4 C C2 N Y N 0 2.254 1.155 -0.182
3 C5 C C3 N Y N 0 2.373 -0.205 0.051
4 C6 C C4 N Y N 0 1.234 -0.973 0.236
5 C3 C C5 N Y N 0 1.01 1.747 -0.238
6 C2 C C6 N Y N 0 -0.139 0.98 -0.052
7 C1 C C7 N N N 0 -2.297 0.291 0.162
8 F F F1 N N N 0 3.594 -0.781 0.097
9 C C C8 S N N 0 -1.411 -0.923 0.343
10 O O O1 N N N 0 -1.686 -1.898 -0.664
11 N N N1 N N N 0 -1.488 1.341 -0.06
12 O1 O O2 N N N 0 -3.508 0.312 0.209
13 H4 H H1 N N N 0 3.141 1.754 -0.327
14 H5 H H2 N N N 0 1.321 -2.034 0.418
15 H3 H H3 N N N 0 0.925 2.808 -0.42
16 H1 H H4 N N N 0 -1.546 -1.352 1.336
17 H H H5 N N N 0 -2.573 -2.279 -0.611
18 H2 H H6 N N N 0 -1.805 2.246 -0.209



D4Y : Chemical Bonds

Total Number of Bonds: 19
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F C5 F C sing 1.35 N N
2 C5 C6 C C doub 1.39 N Y
3 C5 C4 C C sing 1.38 N Y
4 C6 C7 C C sing 1.38 N Y
5 C4 C3 C C doub 1.38 N Y
6 C7 C C C sing 1.51 N N
7 C7 C2 C C doub 1.39 N Y
8 C3 C2 C C sing 1.39 N Y
9 C O C O sing 1.43 N N
10 C C1 C C sing 1.51 N N
11 C2 N C N sing 1.4 N N
12 N C1 N C sing 1.34 N N
13 C1 O1 C O doub 1.21 N N
14 C4 H4 C H sing 1.08 N N
15 C6 H5 C H sing 1.08 N N
16 C3 H3 C H sing 1.08 N N
17 C H1 C H sing 1.09 N N
18 O H O H sing 0.97 N N
19 N H2 N H sing 0.97 N N



D4Y : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
D4Y 6axa Open in New Window Bound ligand 1 1