Chemical Components in the PDB

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JPT : Summary

Code

JPT

One-letter code

X

Molecule name

6-(hydroxymethyl)-3-oxidanyl-2-(thiophen-3-ylmethyl)pyran-4-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 6-(hydroxymethyl)-3-oxidanyl-2-(thiophen-3-ylmethyl)pyran-4-one

Formula

C11 H10 O4 S

Formal charge

0

Molecular weight

238.26 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OCC1=CC(=O)C(=C(Cc2cscc2)O1)O
SMILES OpenEye OEToolkits 2.0.7 c1cscc1CC2=C(C(=O)C=C(O2)CO)O
Canonical SMILES CACTVS 3.385 OCC1=CC(=O)C(=C(Cc2cscc2)O1)O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cscc1CC2=C(C(=O)C=C(O2)CO)O

IUPAC InChI

InChI=1S/C11H10O4S/c12-5-8-4-9(13)11(14)10(15-8)3-7-1-2-16-6-7/h1-2,4,6,12,14H,3,5H2

IUPAC InChI key

ULVBQNJLQXBOPK-UHFFFAOYSA-N
JPT

wwPDB Information

Atom count

26 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-15

Last modified at

2020-01-17

Status

Released

Obsoleted

Not Assigned



JPT : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C7 C C1 N N N 0 -0.77 -0.239 -1.559
2 C8 C C2 N Y N 0 -1.96 0.0050 -0.667
3 C11 C C3 N Y N 0 -2.397 1.231 -0.374
4 S2 S S1 N Y N 0 -3.795 1.121 0.687
5 C12 C C4 N Y N 0 -3.705 -0.635 0.672
6 C13 C C5 N Y N 0 -2.686 -1.025 -0.095
7 C6 C C6 N N N 0 2.888 2.185 0.649
8 O3 O O1 N N N 0 3.365 2.784 -0.557
9 C5 C C7 N N N 0 0.958 -1.48 -0.301
10 C4 C C8 N N N 0 0.483 -0.287 -0.723
11 O4 O O2 N N N 0 0.314 -2.634 -0.625
12 C1 C C9 N N N 0 2.145 -1.509 0.482
13 O2 O O3 N N N 0 2.61 -2.566 0.878
14 C2 C C10 N N N 0 2.774 -0.276 0.788
15 C3 C C11 N N N 0 2.228 0.869 0.33
16 O1 O O4 N N N 0 1.112 0.853 -0.409
17 H7 H H1 N N N 0 -0.896 -1.188 -2.08
18 H1 H H2 N N N 0 -0.69 0.567 -2.288
19 H11 H H3 N N N 0 -1.958 2.151 -0.733
20 H12 H H4 N N N 0 -4.376 -1.298 1.199
21 H13 H H5 N N N 0 -2.44 -2.065 -0.25
22 H62 H H6 N N N 0 3.724 2.017 1.327
23 H61 H H7 N N N 0 2.164 2.849 1.123
24 H3 H H8 N N N 0 3.802 3.636 -0.427
25 H4 H H11 N N N 0 0.735 -3.431 -0.274
26 H2 H H12 N N N 0 3.677 -0.254 1.38



JPT : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C6 O C sing 1.43 N N
2 C6 C3 C C sing 1.51 N N
3 C3 O1 C O sing 1.34 N N
4 C3 C2 C C doub 1.35 N N
5 O1 C4 O C sing 1.34 N N
6 C2 C1 C C sing 1.42 N N
7 C13 C12 C C doub 1.33 N Y
8 C13 C8 C C sing 1.38 N Y
9 C12 S2 C S sing 1.76 N Y
10 C4 C7 C C sing 1.51 N N
11 C4 C5 C C doub 1.35 N N
12 C1 C5 C C sing 1.42 N N
13 C1 O2 C O doub 1.22 N N
14 C8 C7 C C sing 1.51 N N
15 C8 C11 C C doub 1.33 N Y
16 C5 O4 C O sing 1.36 N N
17 S2 C11 S C sing 1.76 N Y
18 C7 H7 C H sing 1.09 N N
19 C7 H1 C H sing 1.09 N N
20 C11 H11 C H sing 1.08 N N
21 C12 H12 C H sing 1.08 N N
22 C13 H13 C H sing 1.08 N N
23 C6 H62 C H sing 1.09 N N
24 C6 H61 C H sing 1.09 N N
25 O3 H3 O H sing 0.97 N N
26 O4 H4 O H sing 0.97 N N
27 C2 H2 C H sing 1.08 N N



JPT : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JPT 6r1v Open in New Window Bound ligand 1 1