Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

W6R : Summary

Code

W6R

One-letter code

X

Molecule name

N-[(thiophen-2-yl)methyl]butanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(thiophen-2-yl)methyl]butanamide
OpenEye OEToolkits 2.0.7 ~{N}-(thiophen-2-ylmethyl)butanamide

Formula

C9 H13 N O S

Formal charge

0

Molecular weight

183.271 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCc1cccs1)CCC
SMILES CACTVS 3.385 CCCC(=O)NCc1sccc1
SMILES OpenEye OEToolkits 2.0.7 CCCC(=O)NCc1cccs1
Canonical SMILES CACTVS 3.385 CCCC(=O)NCc1sccc1
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCC(=O)NCc1cccs1

IUPAC InChI

InChI=1S/C9H13NOS/c1-2-4-9(11)10-7-8-5-3-6-12-8/h3,5-6H,2,4,7H2,1H3,(H,10,11)

IUPAC InChI key

GQINGVFITOTQOL-UHFFFAOYSA-N
W6R

wwPDB Information

Atom count

25 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-09-02

Last modified at

2022-10-28

Status

Released

Obsoleted

Not Assigned



W6R : Atoms of Molecule

Total Number of Atoms: 25
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C7 C C1 N Y N 0 -3.687 0.065 -1.274
2 C8 C C2 N Y N 0 -4.044 0.717 -0.166
3 C1 C C3 N N N 0 4.332 0.047 0.029
4 C5 C C4 N Y N 0 -1.809 -0.417 -0.051
5 C6 C C5 N Y N 0 -2.454 -0.561 -1.21
6 C4 C C6 N N N 0 -0.456 -0.998 0.269
7 C3 C C7 N N N 0 1.885 -0.347 0.09
8 C2 C C8 N N N 0 2.959 0.637 -0.296
9 O O O1 N N N 0 2.189 -1.416 0.577
10 C C C9 N N N 0 5.422 1.047 -0.363
11 N N N1 N N N 0 0.587 -0.041 -0.106
12 S S S1 N Y N 0 -2.78 0.556 1.047
13 H1 H H1 N N N 0 -4.314 0.025 -2.152
14 H2 H H2 N N N 0 -4.967 1.262 -0.035
15 H3 H H3 N N N 0 4.396 -0.16 1.097
16 H4 H H4 N N N 0 4.471 -0.879 -0.529
17 H5 H H5 N N N 0 -2.045 -1.123 -2.036
18 H6 H H6 N N N 0 -0.393 -1.204 1.337
19 H7 H H7 N N N 0 -0.318 -1.924 -0.289
20 H8 H H8 N N N 0 2.82 1.563 0.262
21 H9 H H9 N N N 0 2.895 0.844 -1.364
22 H10 H H10 N N N 0 6.401 0.626 -0.131
23 H11 H H11 N N N 0 5.359 1.253 -1.431
24 H12 H H12 N N N 0 5.284 1.973 0.195
25 H13 H H13 N N N 0 0.344 0.814 -0.495



W6R : Chemical Bonds

Total Number of Bonds: 25
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 C8 C C doub 1.33 N Y
2 C7 C6 C C sing 1.38 N Y
3 C8 S C S sing 1.76 N Y
4 C6 C5 C C doub 1.33 N Y
5 S C5 S C sing 1.76 N Y
6 C5 C4 C C sing 1.51 N N
7 C4 N C N sing 1.46 N N
8 N C3 N C sing 1.35 N N
9 O C3 O C doub 1.21 N N
10 C C1 C C sing 1.53 N N
11 C3 C2 C C sing 1.51 N N
12 C1 C2 C C sing 1.53 N N
13 C7 H1 C H sing 1.08 N N
14 C8 H2 C H sing 1.08 N N
15 C1 H3 C H sing 1.09 N N
16 C1 H4 C H sing 1.09 N N
17 C6 H5 C H sing 1.08 N N
18 C4 H6 C H sing 1.09 N N
19 C4 H7 C H sing 1.09 N N
20 C2 H8 C H sing 1.09 N N
21 C2 H9 C H sing 1.09 N N
22 C H10 C H sing 1.09 N N
23 C H11 C H sing 1.09 N N
24 C H12 C H sing 1.09 N N
25 N H13 N H sing 0.97 N N



W6R : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
W6R 7fol Open in New Window Bound ligand 1 1