Chemical Components in the PDB

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XT9 : Summary

Code

XT9

One-letter code

X

Molecule name

6beta-amino-17-propyl-5alpha,9alpha,13alpha-4,5-epoxymorphinan-3,14-diol

Systematic names

ProgramVersionName
ACDLabs 12.01 6beta-amino-17-propyl-5alpha,9alpha,13alpha-4,5-epoxymorphinan-3,14-diol
OpenEye OEToolkits 2.0.7 (4~{S},4~{a}~{S},7~{R},7~{a}~{R},12~{b}~{R})-7-azanyl-3-propyl-1,2,4,5,6,7,7~{a},13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinoline-4~{a},9-diol

Formula

C19 H26 N2 O3

Formal charge

0

Molecular weight

330.421 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Oc1ccc2CC3N(CCC45C(Oc1c24)C(N)CCC35O)CCC
SMILES CACTVS 3.385 CCCN1CC[C]23[CH]4Oc5c(O)ccc(C[CH]1[C]2(O)CC[CH]4N)c35
SMILES OpenEye OEToolkits 2.0.7 CCCN1CCC23c4c5ccc(c4OC2C(CCC3(C1C5)O)N)O
Canonical SMILES CACTVS 3.385 CCCN1CC[C@@]23[C@H]4Oc5c(O)ccc(C[C@H]1[C@]2(O)CC[C@H]4N)c35
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCN1CC[C@@]23c4c5ccc(c4O[C@H]2[C@@H](CC[C@]3([C@@H]1C5)O)N)O

IUPAC InChI

InChI=1S/C19H26N2O3/c1-2-8-21-9-7-18-15-11-3-4-13(22)16(15)24-17(18)12(20)5-6-19(18,23)14(21)10-11/h3-4,12,14,17,22-23H,2,5-10,20H2,1H3/t12-,14+,17+,18-,19-/m1/s1

IUPAC InChI key

SZCSIOFISXRVGM-UBDCPRGSSA-N
XT9

wwPDB Information

Atom count

50 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-12-07

Last modified at

2024-10-02

Status

Released

Obsoleted

Not Assigned



XT9 : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C29 C C1 R N N 0 -1.458 -2.652 -0.615
2 C30 C C2 N N N 0 -0.509 -3.276 0.429
3 C31 C C3 N N N 0 0.748 -2.453 0.718
4 C32 C C4 R N N 0 -1.784 -1.26 -0.146
5 C33 C C5 R N N 0 -0.423 -0.546 -0.12
6 C34 C C6 S N N 0 0.381 -1.012 1.097
7 C36 C C7 S N N 0 1.563 -0.05 1.159
8 C37 C C8 N N N 0 1.163 1.409 1.365
9 C38 C C9 N N N 0 0.384 -0.722 -1.391
10 C39 C C10 N N N 0 1.646 0.147 -1.276
11 C41 C C11 N N N 0 3.619 0.585 0.054
12 C45 C C15 N Y N 0 -0.132 1.816 0.745
13 C42 C C12 N N N 0 4.576 0.174 -1.068
14 C43 C C13 N N N 0 5.869 0.984 -0.958
15 C44 C C14 N Y N 0 -0.862 0.858 0.081
16 C46 C C16 N Y N 0 -0.746 3.053 0.787
17 C47 C C17 N Y N 0 -2.01 3.214 0.236
18 C48 C C18 N Y N 0 -2.753 2.195 -0.362
19 C50 C C19 N Y N 0 -2.156 0.937 -0.426
20 N28 N N1 N N N 0 -2.689 -3.448 -0.711
21 N40 N N2 N N N 0 2.378 -0.194 -0.052
22 O35 O O1 N N N 0 -0.405 -0.973 2.29
23 O49 O O2 N N N 0 -4.0 2.418 -0.858
24 O51 O O3 N N N 0 -2.569 -0.303 -0.837
25 H1 H H1 N N N 0 -0.967 -2.61 -1.587
26 H2 H H2 N N N 0 -1.059 -3.406 1.361
27 H3 H H3 N N N 0 -0.203 -4.26 0.073
28 H4 H H4 N N N 0 1.295 -2.911 1.542
29 H5 H H5 N N N 0 1.38 -2.44 -0.169
30 H6 H H6 N N N 0 -2.15 -1.318 0.879
31 H7 H H7 N N N 0 2.189 -0.346 2.001
32 H8 H H8 N N N 0 1.104 1.598 2.437
33 H9 H H9 N N N 0 1.95 2.04 0.952
34 H10 H H10 N N N 0 0.667 -1.769 -1.505
35 H11 H H11 N N N 0 -0.206 -0.403 -2.25
36 H12 H H12 N N N 0 2.286 -0.029 -2.141
37 H13 H H13 N N N 0 1.361 1.198 -1.247
38 H14 H H14 N N N 0 4.088 0.393 1.019
39 H15 H H15 N N N 0 3.391 1.647 -0.035
40 H16 H H16 N N N 0 4.804 -0.888 -0.98
41 H17 H H17 N N N 0 4.107 0.366 -2.033
42 H18 H H18 N N N 0 5.64 2.046 -1.046
43 H19 H H19 N N N 0 6.337 0.793 0.007
44 H20 H H20 N N N 0 6.55 0.692 -1.757
45 H21 H H21 N N N 0 -0.244 3.891 1.248
46 H22 H H22 N N N 0 -2.45 4.2 0.273
47 H23 H H23 N N N 0 -2.49 -4.386 -1.025
48 H24 H H24 N N Y 0 -3.183 -3.458 0.169
49 H27 H H27 N N N 0 0.037 -1.35 3.064
50 H28 H H28 N N N 0 -4.011 2.688 -1.787



XT9 : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O51 C32 O C sing 1.42 N N
2 O51 C50 O C sing 1.37 N N
3 O49 C48 O C sing 1.36 N N
4 C29 N28 C N sing 1.47 N N
5 C29 C32 C C sing 1.5 N N
6 C29 C30 C C sing 1.54 N N
7 C32 C33 C C sing 1.54 N N
8 C30 C31 C C sing 1.53 N N
9 C50 C48 C C doub 1.39 N Y
10 C50 C44 C C sing 1.39 N Y
11 C48 C47 C C sing 1.4 N Y
12 C33 C38 C C sing 1.52 N N
13 C33 C44 C C sing 1.48 N N
14 C33 C34 C C sing 1.53 N N
15 C38 C39 C C sing 1.54 N N
16 C44 C45 C C doub 1.38 N Y
17 C47 C46 C C doub 1.39 N Y
18 C31 C34 C C sing 1.53 N N
19 C34 O35 C O sing 1.43 N N
20 C34 C36 C C sing 1.53 N N
21 C45 C46 C C sing 1.38 N Y
22 C45 C37 C C sing 1.49 N N
23 C39 N40 C N sing 1.47 N N
24 N40 C36 N C sing 1.47 N N
25 N40 C41 N C sing 1.47 N N
26 C36 C37 C C sing 1.53 N N
27 C42 C41 C C sing 1.53 N N
28 C42 C43 C C sing 1.53 N N
29 C29 H1 C H sing 1.09 N N
30 C30 H2 C H sing 1.09 N N
31 C30 H3 C H sing 1.09 N N
32 C31 H4 C H sing 1.09 N N
33 C31 H5 C H sing 1.09 N N
34 C32 H6 C H sing 1.09 N N
35 C36 H7 C H sing 1.09 N N
36 C37 H8 C H sing 1.09 N N
37 C37 H9 C H sing 1.09 N N
38 C38 H10 C H sing 1.09 N N
39 C38 H11 C H sing 1.09 N N
40 C39 H12 C H sing 1.09 N N
41 C39 H13 C H sing 1.09 N N
42 C41 H14 C H sing 1.09 N N
43 C41 H15 C H sing 1.09 N N
44 C42 H16 C H sing 1.09 N N
45 C42 H17 C H sing 1.09 N N
46 C43 H18 C H sing 1.09 N N
47 C43 H19 C H sing 1.09 N N
48 C43 H20 C H sing 1.09 N N
49 C46 H21 C H sing 1.08 N N
50 C47 H22 C H sing 1.08 N N
51 N28 H23 N H sing 1.01 N N
52 N28 H24 N H sing 1.01 N N
53 O35 H27 O H sing 0.97 N N
54 O49 H28 O H sing 0.97 N N



XT9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XT9 8feg Open in New Window Polymer component 1 1