Chemical Components in the PDB

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9CF : Summary

Code

9CF

One-letter code

X

Molecule name

(3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one
OpenEye OEToolkits 2.0.6 (3~{S})-3-[[(2~{R},6~{R})-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one

Formula

C16 H20 O5

Formal charge

0

Molecular weight

292.327 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1C(OC(CC1)C)CC2OC(=O)c3c(cc(cc3C2)O)O
SMILES CACTVS 3.385 C[CH]1CCC[CH](C[CH]2Cc3cc(O)cc(O)c3C(=O)O2)O1
SMILES OpenEye OEToolkits 2.0.6 CC1CCCC(O1)CC2Cc3cc(cc(c3C(=O)O2)O)O
Canonical SMILES CACTVS 3.385 C[C@@H]1CCC[C@H](C[C@@H]2Cc3cc(O)cc(O)c3C(=O)O2)O1
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@@H]1CCC[C@@H](O1)C[C@@H]2Cc3cc(cc(c3C(=O)O2)O)O

IUPAC InChI

InChI=1S/C16H20O5/c1-9-3-2-4-12(20-9)8-13-6-10-5-11(17)7-14(18)15(10)16(19)21-13/h5,7,9,12-13,17-18H,2-4,6,8H2,1H3/t9-,12-,13+/m1/s1

IUPAC InChI key

WOMKDMUZNBFXKG-WQAKAFBOSA-N
9CF

wwPDB Information

Atom count

41 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-03-14

Last modified at

2018-06-22

Status

Released

Obsoleted

Not Assigned



9CF : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C15 C C1 N N N 0 4.047 1.85 -0.024
2 C14 C C2 N N N 0 5.272 1.106 -0.566
3 C13 C C3 N N N 0 5.318 -0.295 0.052
4 C12 C C4 R N N 0 4.009 -1.025 -0.26
5 C16 C C5 N N N 0 4.023 -2.404 0.404
6 O5 O O1 N N N 0 2.909 -0.265 0.244
7 C11 C C6 R N N 0 2.788 1.037 -0.333
8 C10 C C7 N N N 0 1.566 1.744 0.258
9 C7 C C8 S N N 0 0.296 0.999 -0.156
10 C6 C C9 N N N 0 -0.931 1.771 0.333
11 O3 O O2 N N N 0 0.296 -0.331 0.439
12 C8 C C10 N N N 0 -0.765 -1.104 0.089
13 O4 O O3 N N N 0 -0.629 -2.282 -0.177
14 C9 C C11 N Y N 0 -2.088 -0.453 0.046
15 C5 C C12 N Y N 0 -2.174 0.939 0.16
16 C4 C C13 N Y N 0 -3.398 1.547 0.114
17 C3 C C14 N Y N 0 -4.555 0.79 -0.042
18 O2 O O4 N N N 0 -5.763 1.407 -0.086
19 C2 C C15 N Y N 0 -4.483 -0.59 -0.154
20 C1 C C16 N Y N 0 -3.25 -1.221 -0.11
21 O1 O O5 N N N 0 -3.168 -2.571 -0.216
22 H1 H H1 N N N 0 4.145 1.975 1.054
23 H2 H H2 N N N 0 3.975 2.829 -0.499
24 H3 H H3 N N N 0 5.198 1.024 -1.65
25 H4 H H4 N N N 0 6.177 1.653 -0.302
26 H5 H H5 N N N 0 6.155 -0.851 -0.37
27 H6 H H6 N N N 0 5.442 -0.213 1.132
28 H7 H H7 N N N 0 3.907 -1.143 -1.339
29 H8 H H8 N N N 0 4.126 -2.286 1.483
30 H9 H H9 N N N 0 3.092 -2.924 0.183
31 H10 H H10 N N N 0 4.863 -2.983 0.021
32 H11 H H11 N N N 0 2.669 0.947 -1.413
33 H12 H H12 N N N 0 1.643 1.755 1.345
34 H13 H H13 N N N 0 1.524 2.768 -0.114
35 H14 H H14 N N N 0 0.262 0.912 -1.242
36 H15 H H15 N N N 0 -0.805 2.017 1.387
37 H16 H H16 N N N 0 -1.03 2.692 -0.242
38 H17 H H17 N N N 0 -3.467 2.621 0.201
39 H18 H H18 N N N 0 -6.043 1.661 -0.976
40 H19 H H19 N N N 0 -5.385 -1.172 -0.274
41 H20 H H20 N N N 0 -3.213 -3.035 0.631



9CF : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C16 C12 C C sing 1.53 N N
2 C13 C12 C C sing 1.53 N N
3 C13 C14 C C sing 1.53 N N
4 C12 O5 C O sing 1.43 N N
5 C14 C15 C C sing 1.53 N N
6 O5 C11 O C sing 1.43 N N
7 C15 C11 C C sing 1.53 N N
8 C11 C10 C C sing 1.53 N N
9 C10 C7 C C sing 1.53 N N
10 C6 C7 C C sing 1.53 N N
11 C6 C5 C C sing 1.51 N N
12 C7 O3 C O sing 1.46 N N
13 C4 C5 C C doub 1.37 N Y
14 C4 C3 C C sing 1.39 N Y
15 C5 C9 C C sing 1.4 N Y
16 O3 C8 O C sing 1.36 N N
17 O2 C3 O C sing 1.36 N N
18 C3 C2 C C doub 1.39 N Y
19 C9 C8 C C sing 1.48 N N
20 C9 C1 C C doub 1.4 N Y
21 C8 O4 C O doub 1.22 N N
22 C2 C1 C C sing 1.39 N Y
23 C1 O1 C O sing 1.36 N N
24 C15 H1 C H sing 1.09 N N
25 C15 H2 C H sing 1.09 N N
26 C14 H3 C H sing 1.09 N N
27 C14 H4 C H sing 1.09 N N
28 C13 H5 C H sing 1.09 N N
29 C13 H6 C H sing 1.09 N N
30 C12 H7 C H sing 1.09 N N
31 C16 H8 C H sing 1.09 N N
32 C16 H9 C H sing 1.09 N N
33 C16 H10 C H sing 1.09 N N
34 C11 H11 C H sing 1.09 N N
35 C10 H12 C H sing 1.09 N N
36 C10 H13 C H sing 1.09 N N
37 C7 H14 C H sing 1.09 N N
38 C6 H15 C H sing 1.09 N N
39 C6 H16 C H sing 1.09 N N
40 C4 H17 C H sing 1.08 N N
41 O2 H18 O H sing 0.97 N N
42 C2 H19 C H sing 1.08 N N
43 O1 H20 O H sing 0.97 N N



9CF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9CF 5zh3 Open in New Window Bound ligand 2 1