Chemical Components in the PDB

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Z47 : Summary

Code

Z47

One-letter code

X

Molecule name

(2R,3S,4R,5S,6R)-2-(HYDROXYMETHYL)-6-[3-(NAPHTHALEN-1-YL)PROPYL]OXANE-3,4,5-TRIOL

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-(3-naphthalen-1-ylpropyl)oxane-3,4,5-triol

Formula

C19 H24 O5

Formal charge

0

Molecular weight

332.391 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC[CH]1O[CH](CCCc2cccc3ccccc23)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)cccc2CCCC3C(C(C(C(O3)CO)O)O)O
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@@H](CCCc2cccc3ccccc23)[C@H](O)[C@@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)cccc2CCC[C@@H]3[C@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O

IUPAC InChI

InChI=1S/C19H24O5/c20-11-16-18(22)19(23)17(21)15(24-16)10-4-8-13-7-3-6-12-5-1-2-9-14(12)13/h1-3,5-7,9,15-23H,4,8,10-11H2/t15-,16+,17+,18-,19+/m0/s1

IUPAC InChI key

RCVLTURVGCLYEX-BRIYLRKRSA-N
Z47

wwPDB Information

Atom count

48 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-08-10

Last modified at

2016-03-04

Status

Released

Obsoleted

Not Assigned



Z47 : Atoms of Molecule

Total Number of Atoms: 48
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 -1.842 -1.086 0.682
2 C2 C C2 R N N 0 -3.106 -1.832 0.248
3 C3 C C3 R N N 0 -3.853 -0.992 -0.792
4 C4 C C4 R N N 0 -4.167 0.382 -0.192
5 C5 C C5 R N N 0 -2.862 1.043 0.259
6 C6 C C6 N N N 0 -3.172 2.39 0.915
7 O2 O O2 N N N 0 -3.947 -2.047 1.382
8 O3 O O3 N N N 0 -5.072 -1.647 -1.15
9 O4 O O4 N N N 0 -4.8 1.201 -1.178
10 O5 O O5 N N N 0 -2.202 0.196 1.202
11 O6 O O6 N N N 0 -1.949 3.059 1.231
12 C7 C C7 N N N 0 -0.915 -0.906 -0.522
13 C8 C C8 N N N 0 0.4 -0.273 -0.064
14 C9 C C9 N N N 0 1.326 -0.093 -1.268
15 C10 C C10 N Y N 0 2.621 0.531 -0.817
16 C15 C C15 N Y N 0 2.795 1.879 -0.895
17 C14 C C14 N Y N 0 3.986 2.474 -0.483
18 C13 C C13 N Y N 0 5.01 1.724 0.01
19 C12 C C12 N Y N 0 4.867 0.33 0.106
20 C11 C C11 N Y N 0 3.654 -0.275 -0.309
21 C16 C C16 N Y N 0 5.902 -0.477 0.611
22 C17 C C17 N Y N 0 5.727 -1.824 0.689
23 C18 C C18 N Y N 0 4.537 -2.419 0.276
24 C19 C C19 N Y N 0 3.509 -1.669 -0.208
25 H21 H H21 N N N 0 -1.328 -1.66 1.454
26 H22 H H22 N N N 0 -2.83 -2.792 -0.19
27 H23 H H23 N N N 0 -3.23 -0.869 -1.678
28 H24 H H24 N N N 0 -4.83 0.263 0.664
29 H71C H H71C N N N 0 -0.713 -1.878 -0.973
30 H72C H H72C N N N 0 -1.395 -0.258 -1.256
31 H2 H H2 N N N 0 -4.769 -2.516 1.179
32 H3 H H3 N N N 0 -5.597 -1.169 -1.806
33 H5 H H5 N N N 0 -2.215 1.199 -0.604
34 H4 H H4 N N N 0 -5.027 2.087 -0.866
35 H61C H H61C N N N 0 -3.754 3.003 0.226
36 H82C H H82C N N N 0 0.879 -0.921 0.67
37 H62C H H62C N N N 0 -3.744 2.227 1.828
38 H6 H H6 N N N 0 -2.07 3.922 1.65
39 H81C H H81C N N N 0 0.197 0.699 0.387
40 H91C H H91C N N N 0 1.528 -1.065 -1.719
41 H92C H H92C N N N 0 0.846 0.555 -2.002
42 H15 H H15 N N N 0 1.998 2.496 -1.283
43 H14 H H14 N N N 0 4.098 3.545 -0.556
44 H13 H H13 N N N 0 5.927 2.199 0.326
45 H16 H H16 N N N 0 6.83 -0.03 0.934
46 H19 H H19 N N N 0 2.592 -2.144 -0.524
47 H17 H H17 N N N 0 6.524 -2.442 1.077
48 H18 H H18 N N N 0 4.424 -3.491 0.349



Z47 : 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 C1 C2 C C sing 1.53 N N
2 C1 O5 C O sing 1.43 N N
3 C1 C7 C C sing 1.53 N N
4 C2 C3 C C sing 1.53 N N
5 C2 O2 C O sing 1.43 N N
6 C3 C4 C C sing 1.53 N N
7 C3 O3 C O sing 1.43 N N
8 C4 C5 C C sing 1.53 N N
9 C4 O4 C O sing 1.43 N N
10 C5 C6 C C sing 1.53 N N
11 C5 O5 C O sing 1.43 N N
12 C6 O6 C O sing 1.43 N N
13 C7 C8 C C sing 1.53 N N
14 C8 C9 C C sing 1.53 N N
15 C9 C10 C C sing 1.51 N N
16 C10 C15 C C sing 1.36 N Y
17 C10 C11 C C doub 1.41 N Y
18 C15 C14 C C doub 1.39 N Y
19 C14 C13 C C sing 1.36 N Y
20 C13 C12 C C doub 1.4 N Y
21 C12 C11 C C sing 1.42 N Y
22 C12 C16 C C sing 1.41 N Y
23 C11 C19 C C sing 1.41 N Y
24 C16 C17 C C doub 1.36 N Y
25 C17 C18 C C sing 1.39 N Y
26 C18 C19 C C doub 1.36 N Y
27 C1 H21 C H sing 1.09 N N
28 C2 H22 C H sing 1.09 N N
29 C3 H23 C H sing 1.09 N N
30 C4 H24 C H sing 1.09 N N
31 C7 H71C C H sing 1.09 N N
32 C7 H72C C H sing 1.09 N N
33 O2 H2 O H sing 0.97 N N
34 O3 H3 O H sing 0.97 N N
35 C5 H5 C H sing 1.09 N N
36 O4 H4 O H sing 0.97 N N
37 C6 H61C C H sing 1.09 N N
38 C6 H62C C H sing 1.09 N N
39 O6 H6 O H sing 0.97 N N
40 C8 H81C C H sing 1.09 N N
41 C8 H82C C H sing 1.09 N N
42 C9 H91C C H sing 1.09 N N
43 C9 H92C C H sing 1.09 N N
44 C15 H15 C H sing 1.08 N N
45 C14 H14 C H sing 1.08 N N
46 C13 H13 C H sing 1.08 N N
47 C16 H16 C H sing 1.08 N N
48 C19 H19 C H sing 1.08 N N
49 C17 H17 C H sing 1.08 N N
50 C18 H18 C H sing 1.08 N N



Z47 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Z47 5abz Open in New Window Bound ligand 2 1