Chemical Components in the PDB

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D9M : Summary

Code

D9M

One-letter code

X

Molecule name

(1S,2S,3S,4R,5R)-4-(morpholin-4-yl)-2-[(pyridin-4-ylmethyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol

Systematic names

ProgramVersionName
ACDLabs 12.01 (1S,2S,3S,4R,5R)-4-(morpholin-4-yl)-2-[(pyridin-4-ylmethyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)
OpenEye OEToolkits 2.0.6 (1~{S},2~{S},3~{S},4~{R},5~{R})-4-morpholin-4-yl-2-(pyridin-4-ylmethylamino)-6,8-dioxabicyclo[3.2.1]octan-3-ol

Formula

C16 H23 N3 O4

Formal charge

0

Molecular weight

321.372 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O1CCN(CC1)C3C4OCC(C(NCc2ccncc2)C3O)O4
SMILES CACTVS 3.385 O[CH]1[CH](NCc2ccncc2)[CH]3CO[CH](O3)[CH]1N4CCOCC4
SMILES OpenEye OEToolkits 2.0.6 c1cnccc1CNC2C3COC(O3)C(C2O)N4CCOCC4
Canonical SMILES CACTVS 3.385 O[C@H]1[C@H](NCc2ccncc2)[C@H]3CO[C@H](O3)[C@@H]1N4CCOCC4
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cnccc1CN[C@@H]2[C@H]3CO[C@H](O3)[C@@H]([C@H]2O)N4CCOCC4

IUPAC InChI

InChI=1S/C16H23N3O4/c20-15-13(18-9-11-1-3-17-4-2-11)12-10-22-16(23-12)14(15)19-5-7-21-8-6-19/h1-4,12-16,18,20H,5-10H2/t12-,13-,14-,15+,16-/m1/s1

IUPAC InChI key

RCXMXLJCXLGFHQ-DGXTUMSLSA-N
D9M

wwPDB Information

Atom count

46 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-10-23

Last modified at

2020-04-17

Status

Released

Obsoleted

Not Assigned



D9M : 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 O3 O O1 N N N 0 0.672 -3.703 -0.021
2 C4 C C1 N Y N 0 2.609 1.451 -0.064
3 C5 C C2 N N N 0 1.241 2.05 -0.266
4 C6 C C3 S N N 0 -1.095 1.522 -0.62
5 N1 N N1 N N N 0 0.253 0.974 -0.42
6 C7 C C4 S N N 0 -1.717 1.874 0.742
7 C8 C C5 N N N 0 -3.236 2.071 0.529
8 N2 N N2 N N N 0 -0.963 -1.423 -0.129
9 C9 C C6 R N N 0 -2.722 -0.134 1.001
10 C10 C C7 R N N 0 -2.22 -0.693 -0.34
11 C11 C C8 S N N 0 -1.981 0.474 -1.304
12 C12 C C9 N N N 0 -0.531 -2.095 -1.363
13 C13 C C10 N N N 0 0.809 -2.792 -1.115
14 C14 C C11 N N N 0 0.254 -3.082 1.197
15 C15 C C12 N N N 0 -1.092 -2.388 0.973
16 O2 O O2 N N N 0 -3.233 1.066 -1.657
17 O O O3 N N N 0 -3.811 0.768 0.733
18 O1 O O4 N N N 0 -1.664 0.677 1.558
19 C C C13 N Y N 0 3.074 1.158 1.209
20 C3 C C14 N Y N 0 3.43 1.175 -1.147
21 C2 C C15 N Y N 0 4.678 0.625 -0.923
22 N N N3 N Y N 0 5.089 0.363 0.303
23 C1 C C16 N Y N 0 4.331 0.603 1.355
24 H1 H H1 N N N 0 0.981 2.662 0.598
25 H2 H H2 N N N 0 1.245 2.671 -1.163
26 H3 H H3 N N N 0 -1.039 2.418 -1.239
27 H4 H H4 N N N 0 0.507 0.355 -1.175
28 H6 H H6 N N N 0 -1.232 2.728 1.215
29 H7 H H7 N N N 0 -3.632 2.779 1.258
30 H8 H H8 N N N 0 -3.435 2.421 -0.484
31 H10 H H10 N N N 0 -3.021 -0.925 1.688
32 H11 H H11 N N N 0 -2.968 -1.367 -0.758
33 H12 H H12 N N N 0 -1.484 0.108 -2.202
34 H13 H H13 N N N 0 -1.277 -2.835 -1.655
35 H14 H H14 N N N 0 -0.418 -1.359 -2.158
36 H15 H H15 N N N 0 1.568 -2.047 -0.876
37 H16 H H16 N N N 0 1.105 -3.34 -2.01
38 H17 H H17 N N N 0 0.148 -3.838 1.974
39 H18 H H18 N N N 0 0.996 -2.345 1.503
40 H19 H H19 N N N 0 -1.388 -1.864 1.882
41 H20 H H20 N N N 0 -1.847 -3.131 0.718
42 H21 H H21 N N N 0 -3.157 1.812 -2.267
43 H22 H H22 N N N 0 2.461 1.36 2.075
44 H23 H H23 N N N 0 3.098 1.387 -2.152
45 H24 H H24 N N N 0 5.323 0.407 -1.76
46 H25 H H25 N N N 0 4.701 0.372 2.343



D9M : Chemical Bonds

Total Number of Bonds: 49
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C13 O C sing 1.43 N N
2 O3 C14 O C sing 1.43 N N
3 O2 C11 O C sing 1.43 N N
4 C13 C12 C C sing 1.53 N N
5 C1 C C C doub 1.38 N Y
6 C1 N C N sing 1.32 N Y
7 C C4 C C sing 1.39 N Y
8 C14 C15 C C sing 1.53 N N
9 N2 C12 N C sing 1.47 N N
10 N2 C15 N C sing 1.47 N N
11 N2 C10 N C sing 1.47 N N
12 N C2 N C doub 1.32 N Y
13 C5 C4 C C sing 1.51 N N
14 C5 N1 C N sing 1.47 N N
15 C4 C3 C C doub 1.39 N Y
16 C11 C10 C C sing 1.53 N N
17 C11 C6 C C sing 1.53 N N
18 C10 C9 C C sing 1.54 N N
19 C2 C3 C C sing 1.38 N Y
20 C6 N1 C N sing 1.47 N N
21 C6 C7 C C sing 1.54 N N
22 C9 O C O sing 1.44 N N
23 C9 O1 C O sing 1.44 N N
24 O C8 O C sing 1.44 N N
25 C7 O1 C O sing 1.45 N N
26 C7 C8 C C sing 1.55 N N
27 C5 H1 C H sing 1.09 N N
28 C5 H2 C H sing 1.09 N N
29 C6 H3 C H sing 1.09 N N
30 N1 H4 N H sing 1.01 N N
31 C7 H6 C H sing 1.09 N N
32 C8 H7 C H sing 1.09 N N
33 C8 H8 C H sing 1.09 N N
34 C9 H10 C H sing 1.09 N N
35 C10 H11 C H sing 1.09 N N
36 C11 H12 C H sing 1.09 N N
37 C12 H13 C H sing 1.09 N N
38 C12 H14 C H sing 1.09 N N
39 C13 H15 C H sing 1.09 N N
40 C13 H16 C H sing 1.09 N N
41 C14 H17 C H sing 1.09 N N
42 C14 H18 C H sing 1.09 N N
43 C15 H19 C H sing 1.09 N N
44 C15 H20 C H sing 1.09 N N
45 O2 H21 O H sing 0.97 N N
46 C H22 C H sing 1.08 N N
47 C3 H23 C H sing 1.08 N N
48 C2 H24 C H sing 1.08 N N
49 C1 H25 C H sing 1.08 N N



D9M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
D9M 5qbm Open in New Window Bound ligand 1 1