Chemical Components in the PDB

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R0D : Summary

Code

R0D

One-letter code

X

Molecule name

(5-chloro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]methanone

Systematic names

ProgramVersionName
ACDLabs 12.01 (5-chloro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]methanone
OpenEye OEToolkits 2.0.7 (5-chloranylspiro[indole-3,4'-piperidine]-1'-yl)-[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methanone

Formula

C21 H19 Cl N2 O3

Formal charge

0

Molecular weight

382.84 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C3CC2(c1cc(Cl)ccc1N=C2)CCN3C(C5COc4ccccc4O5)=O
SMILES CACTVS 3.385 Clc1ccc2N=CC3(CCN(CC3)C(=O)[CH]4COc5ccccc5O4)c2c1
SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)OCC(O2)C(=O)N3CCC4(CC3)C=Nc5c4cc(cc5)Cl
Canonical SMILES CACTVS 3.385 Clc1ccc2N=CC3(CCN(CC3)C(=O)[C@H]4COc5ccccc5O4)c2c1
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)OC[C@@H](O2)C(=O)N3CCC4(CC3)C=Nc5c4cc(cc5)Cl

IUPAC InChI

InChI=1S/C21H19ClN2O3/c22-14-5-6-16-15(11-14)21(13-23-16)7-9-24(10-8-21)20(25)19-12-26-17-3-1-2-4-18(17)27-19/h1-6,11,13,19H,7-10,12H2/t19-/m1/s1

IUPAC InChI key

FORRKPPZDDUANL-LJQANCHMSA-N
R0D

wwPDB Information

Atom count

46 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-01-21

Last modified at

2020-03-13

Status

Released

Obsoleted

Not Assigned



R0D : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 -0.178 0.979 0.663
2 C13 C C2 R N N 0 -2.705 0.078 -0.297
3 C17 C C3 N Y N 0 -6.261 -0.531 1.695
4 C20 C C4 N Y N 0 -5.962 -1.434 -0.905
5 C21 C C5 N Y N 0 -4.962 -0.67 -0.321
6 C24 C C6 N N N 0 0.489 1.704 -1.667
7 C26 C C7 N Y N 0 3.551 0.24 0.131
8 C04 C C10 N Y N 0 5.717 0.899 0.947
9 C02 C C8 N Y N 0 5.346 -1.335 0.155
10 C03 C C9 N Y N 0 6.185 -0.372 0.688
11 C05 C C11 N Y N 0 4.385 1.225 0.67
12 C07 C C12 N N N 0 2.458 2.32 0.461
13 C08 C C13 N N N 0 2.215 0.916 -0.042
14 C09 C C14 N N N 0 1.149 0.225 0.801
15 C12 C C15 N N N 0 -1.696 0.687 -1.236
16 C14 C C16 N N N 0 -3.174 1.133 0.714
17 C16 C C17 N Y N 0 -5.112 -0.218 0.984
18 C18 C C18 N Y N 0 -7.254 -1.292 1.107
19 C19 C C19 N Y N 0 -7.104 -1.743 -0.192
20 C25 C C20 N N N 0 1.81 0.942 -1.516
21 C27 C C21 N Y N 0 4.023 -1.023 -0.123
22 N06 N N1 N N N 0 3.688 2.39 0.833
23 N11 N N2 N N N 0 -0.505 1.108 -0.764
24 O15 O O1 N N N 0 -4.14 0.526 1.579
25 O22 O O2 N N N 0 -3.846 -0.369 -1.039
26 O23 O O3 N N N 0 -1.954 0.798 -2.415
27 CL01 CL CL1 N N N 0 5.948 -2.931 -0.166
28 H1 H H1 N N N 0 -0.968 0.425 1.17
29 H2 H H2 N N N 0 -0.084 1.97 1.107
30 H3 H H3 N N N 0 -2.257 -0.764 0.23
31 H4 H H4 N N N 0 -6.381 -0.18 2.709
32 H5 H H5 N N N 0 -5.847 -1.788 -1.919
33 H6 H H6 N N N 0 0.639 2.751 -1.406
34 H7 H H7 N N N 0 0.138 1.63 -2.697
35 H8 H H8 N N N 0 7.215 -0.618 0.903
36 H9 H H9 N N N 0 6.379 1.643 1.363
37 H10 H H10 N N N 0 1.733 3.119 0.501
38 H11 H H11 N N N 0 1.458 0.221 1.846
39 H12 H H12 N N N 0 1.021 -0.801 0.456
40 H13 H H13 N N N 0 -2.324 1.483 1.301
41 H14 H H14 N N N 0 -3.628 1.972 0.187
42 H15 H H15 N N N 0 -8.148 -1.534 1.662
43 H16 H H16 N N N 0 -7.881 -2.338 -0.648
44 H17 H H17 N N N 0 1.685 -0.079 -1.877
45 H18 H H18 N N N 0 2.586 1.441 -2.097
46 H19 H H19 N N N 0 3.366 -1.772 -0.538



R0D : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N06 C07 N C doub 1.29 N N
2 N06 C05 N C sing 1.37 N N
3 C07 C08 C C sing 1.51 N N
4 C04 C05 C C doub 1.4 N Y
5 C04 C03 C C sing 1.38 N Y
6 C05 C26 C C sing 1.4 N Y
7 C25 C24 C C sing 1.53 N N
8 C25 C08 C C sing 1.53 N N
9 C24 N11 C N sing 1.47 N N
10 C03 C02 C C doub 1.38 N Y
11 C08 C26 C C sing 1.51 N N
12 C08 C09 C C sing 1.52 N N
13 C26 C27 C C doub 1.37 N Y
14 C02 C27 C C sing 1.39 N Y
15 C02 CL01 C CL sing 1.74 N N
16 N11 C10 N C sing 1.47 N N
17 N11 C12 N C sing 1.35 N N
18 C09 C10 C C sing 1.53 N N
19 O23 C12 O C doub 1.21 N N
20 C12 C13 C C sing 1.51 N N
21 C13 C14 C C sing 1.53 N N
22 C13 O22 C O sing 1.43 N N
23 C14 O15 C O sing 1.43 N N
24 O22 C21 O C sing 1.36 N N
25 O15 C16 O C sing 1.36 N N
26 C21 C16 C C doub 1.39 N Y
27 C21 C20 C C sing 1.39 N Y
28 C16 C17 C C sing 1.39 N Y
29 C20 C19 C C doub 1.38 N Y
30 C17 C18 C C doub 1.38 N Y
31 C19 C18 C C sing 1.38 N Y
32 C10 H1 C H sing 1.09 N N
33 C10 H2 C H sing 1.09 N N
34 C13 H3 C H sing 1.09 N N
35 C17 H4 C H sing 1.08 N N
36 C20 H5 C H sing 1.08 N N
37 C24 H6 C H sing 1.09 N N
38 C24 H7 C H sing 1.09 N N
39 C03 H8 C H sing 1.08 N N
40 C04 H9 C H sing 1.08 N N
41 C07 H10 C H sing 1.08 N N
42 C09 H11 C H sing 1.09 N N
43 C09 H12 C H sing 1.09 N N
44 C14 H13 C H sing 1.09 N N
45 C14 H14 C H sing 1.09 N N
46 C18 H15 C H sing 1.08 N N
47 C19 H16 C H sing 1.08 N N
48 C25 H17 C H sing 1.09 N N
49 C25 H18 C H sing 1.09 N N
50 C27 H19 C H sing 1.08 N N



R0D : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
R0D 6uz8 Open in New Window Bound ligand 4 1