Chemical Components in the PDB

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W0D : Summary

Code

W0D

One-letter code

X

Molecule name

N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide
OpenEye OEToolkits 2.0.7 ~{N}-(1~{H}-benzimidazol-2-ylmethyl)furan-2-carboxamide

Formula

C13 H11 N3 O2

Formal charge

0

Molecular weight

241.245 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n2c(CNC(=O)c1ccco1)nc3ccccc23
SMILES CACTVS 3.385 O=C(NCc1[nH]c2ccccc2n1)c3occc3
SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)[nH]c(n2)CNC(=O)c3ccco3
Canonical SMILES CACTVS 3.385 O=C(NCc1[nH]c2ccccc2n1)c3occc3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)[nH]c(n2)CNC(=O)c3ccco3

IUPAC InChI

InChI=1S/C13H11N3O2/c17-13(11-6-3-7-18-11)14-8-12-15-9-4-1-2-5-10(9)16-12/h1-7H,8H2,(H,14,17)(H,15,16)

IUPAC InChI key

WFEIYWNIMQWEHE-UHFFFAOYSA-N
W0D

wwPDB Information

Atom count

29 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-09-24

Last modified at

2021-01-08

Status

Released

Obsoleted

Not Assigned



W0D : Atoms of Molecule

Total Number of Atoms: 29
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -1.936 0.765 1.062
2 C4 C C1 N Y N 0 -4.227 -0.308 1.38
3 C5 C C2 N Y N 0 -5.253 -0.921 0.694
4 C6 C C3 N Y N 0 -5.168 -1.107 -0.679
5 C7 C C4 N Y N 0 -4.069 -0.687 -1.372
6 C8 C C5 N Y N 0 -3.017 -0.062 -0.698
7 C10 C C6 N Y N 0 4.894 0.106 -0.011
8 O O O1 N N N 0 2.814 2.09 -0.153
9 C C C7 N N N 0 2.505 0.916 -0.067
10 C9 C C8 N Y N 0 3.547 -0.114 0.006
11 O1 O O2 N Y N 0 3.342 -1.444 0.101
12 C12 C C9 N Y N 0 4.523 -2.074 0.146
13 C11 C C10 N Y N 0 5.509 -1.153 0.079
14 N N N2 N N N 0 1.205 0.562 -0.04
15 C1 C C11 N N N 0 0.164 1.59 -0.113
16 C2 C C12 N Y N 0 -1.193 0.936 -0.065
17 N2 N N3 N Y N 0 -1.824 0.452 -1.094
18 C3 C C13 N Y N 0 -3.102 0.126 0.692
19 H1 H H1 N N N 0 -1.689 1.038 1.96
20 H2 H H2 N N N 0 -4.298 -0.166 2.449
21 H3 H H3 N N N 0 -6.129 -1.259 1.228
22 H4 H H4 N N N 0 -5.979 -1.59 -1.204
23 H5 H H5 N N N 0 -4.013 -0.837 -2.441
24 H6 H H6 N N N 0 5.391 1.062 -0.084
25 H7 H H7 N N N 0 4.663 -3.142 0.223
26 H8 H H8 N N N 0 6.571 -1.349 0.088
27 H9 H H9 N N N 0 0.958 -0.374 0.027
28 H10 H H10 N N N 0 0.269 2.273 0.729
29 H11 H H11 N N N 0 0.266 2.145 -1.046



W0D : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 C6 C C doub 1.37 N Y
2 C7 C8 C C sing 1.4 N Y
3 C6 C5 C C sing 1.39 N Y
4 C8 N2 C N sing 1.36 N Y
5 C8 C3 C C doub 1.41 N Y
6 C5 C4 C C doub 1.38 N Y
7 N2 C2 N C doub 1.3 N Y
8 C3 C4 C C sing 1.39 N Y
9 C3 N1 C N sing 1.38 N Y
10 C2 N1 C N sing 1.36 N Y
11 C2 C1 C C sing 1.51 N N
12 C1 N C N sing 1.46 N N
13 N C N C sing 1.35 N N
14 O C O C doub 1.22 N N
15 C C9 C C sing 1.47 N N
16 C9 O1 C O sing 1.35 N Y
17 C9 C10 C C doub 1.36 N Y
18 O1 C12 O C sing 1.34 N Y
19 C10 C11 C C sing 1.4 N Y
20 C12 C11 C C doub 1.35 N Y
21 N1 H1 N H sing 0.97 N N
22 C4 H2 C H sing 1.08 N N
23 C5 H3 C H sing 1.08 N N
24 C6 H4 C H sing 1.08 N N
25 C7 H5 C H sing 1.08 N N
26 C10 H6 C H sing 1.08 N N
27 C12 H7 C H sing 1.08 N N
28 C11 H8 C H sing 1.08 N N
29 N H9 N H sing 0.97 N N
30 C1 H10 C H sing 1.09 N N
31 C1 H11 C H sing 1.09 N N



W0D : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
W0D 5s2t Open in New Window Bound ligand 1 1
W0D 7nbh Open in New Window Bound ligand 6 1