Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

OD2 : Summary

Code

OD2

One-letter code

X

Molecule name

2-[6-(4-methylsulfanylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 2-[6-(4-methylsulfanylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid

Formula

C15 H12 N2 O2 S3

Formal charge

0

Molecular weight

348.463 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CSc1ccc(cc1)c2sc3c(SCC(O)=O)ncnc3c2
SMILES OpenEye OEToolkits 2.0.7 CSc1ccc(cc1)c2cc3c(s2)c(ncn3)SCC(=O)O
Canonical SMILES CACTVS 3.385 CSc1ccc(cc1)c2sc3c(SCC(O)=O)ncnc3c2
Canonical SMILES OpenEye OEToolkits 2.0.7 CSc1ccc(cc1)c2cc3c(s2)c(ncn3)SCC(=O)O

IUPAC InChI

InChI=1S/C15H12N2O2S3/c1-20-10-4-2-9(3-5-10)12-6-11-14(22-12)15(17-8-16-11)21-7-13(18)19/h2-6,8H,7H2,1H3,(H,18,19)

IUPAC InChI key

KJCQGDBVLKOAHP-UHFFFAOYSA-N
OD2

wwPDB Information

Atom count

34 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-02-27

Last modified at

2020-03-06

Status

Released

Obsoleted

Not Assigned



OD2 : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C1 N N N 0 6.211 -1.542 0.001
2 O O O1 N N N 0 5.74 -2.655 0.0
3 O1 O O2 N N N 0 7.543 -1.378 -0.004
4 C1 C C2 N N N 0 5.303 -0.34 0.002
5 S S S1 N N N 0 3.578 -0.886 0.0
6 C2 C C3 N Y N 0 2.762 0.675 0.001
7 N1 N N1 N Y N 0 3.463 1.804 0.002
8 C14 C C4 N Y N 0 2.857 2.977 0.003
9 N N N2 N Y N 0 1.553 3.097 0.003
10 C4 C C5 N Y N 0 0.75 2.006 0.002
11 C5 C C6 N Y N 0 -0.648 1.928 0.001
12 C6 C C7 N Y N 0 -1.157 0.691 0.0
13 S1 S S2 N Y N 0 0.128 -0.506 -0.001
14 C3 C C8 N Y N 0 1.359 0.748 -0.005
15 C7 C C9 N Y N 0 -2.601 0.375 0.0
16 C12 C C10 N Y N 0 -3.543 1.406 -0.005
17 C11 C C11 N Y N 0 -4.888 1.109 -0.005
18 C10 C C12 N Y N 0 -5.309 -0.217 -0.001
19 S2 S S3 N N N 0 -7.03 -0.594 -0.001
20 C13 C C13 N N N 0 -7.051 -2.408 0.006
21 C9 C C14 N Y N 0 -4.373 -1.247 0.004
22 C8 C C15 N Y N 0 -3.026 -0.955 -0.002
23 H1 H H1 N N N 0 8.085 -2.179 -0.008
24 H2 H H2 N N N 0 5.494 0.259 0.892
25 H3 H H3 N N N 0 5.495 0.261 -0.888
26 H4 H H4 N N N 0 3.46 3.873 0.005
27 H5 H H5 N N N 0 -1.274 2.809 0.002
28 H6 H H6 N N N 0 -3.217 2.436 -0.008
29 H7 H H7 N N N 0 -5.616 1.906 -0.009
30 H8 H H8 N N N 0 -6.54 -2.78 -0.882
31 H9 H H9 N N N 0 -6.542 -2.773 0.898
32 H10 H H10 N N N 0 -8.083 -2.759 0.006
33 H11 H H11 N N N 0 -4.702 -2.275 0.007
34 H12 H H12 N N N 0 -2.3 -1.755 -0.002



OD2 : Chemical Bonds

Total Number of Bonds: 36
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N C14 N C doub 1.31 N Y
2 N C4 N C sing 1.35 N Y
3 C14 N1 C N sing 1.32 N Y
4 C12 C11 C C doub 1.38 N Y
5 C12 C7 C C sing 1.4 N Y
6 C11 C10 C C sing 1.39 N Y
7 C5 C4 C C sing 1.4 N Y
8 C5 C6 C C doub 1.34 N Y
9 C4 C3 C C doub 1.4 N Y
10 C6 C7 C C sing 1.48 N N
11 C6 S1 C S sing 1.76 N Y
12 C7 C8 C C doub 1.4 N Y
13 N1 C2 N C doub 1.33 N Y
14 S2 C10 S C sing 1.76 N N
15 S2 C13 S C sing 1.81 N N
16 C10 C9 C C doub 1.39 N Y
17 C3 C2 C C sing 1.4 N Y
18 C3 S1 C S sing 1.76 N Y
19 C2 S C S sing 1.76 N N
20 C8 C9 C C sing 1.38 N Y
21 S C1 S C sing 1.81 N N
22 C1 C C C sing 1.51 N N
23 C O C O doub 1.21 N N
24 C O1 C O sing 1.34 N N
25 O1 H1 O H sing 0.97 N N
26 C1 H2 C H sing 1.09 N N
27 C1 H3 C H sing 1.09 N N
28 C14 H4 C H sing 1.08 N N
29 C5 H5 C H sing 1.08 N N
30 C12 H6 C H sing 1.08 N N
31 C11 H7 C H sing 1.08 N N
32 C13 H8 C H sing 1.09 N N
33 C13 H9 C H sing 1.09 N N
34 C13 H10 C H sing 1.09 N N
35 C9 H11 C H sing 1.08 N N
36 C8 H12 C H sing 1.08 N N



OD2 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
OD2 6y6f Open in New Window Bound ligand 1 1