Chemical Components in the PDB

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WFB : Summary

Code

WFB

One-letter code

X

Molecule name

4,4'-(1H-benzimidazole-2,6-diyl)di(benzene-1-carboximidamide)

Systematic names

ProgramVersionName
ACDLabs 12.01 4,4'-(1H-benzimidazole-2,6-diyl)di(benzene-1-carboximidamide)
OpenEye OEToolkits 2.0.7 4-[2-(4-carbamimidoylphenyl)-3~{H}-benzimidazol-5-yl]benzenecarboximidamide

Formula

C21 H18 N6

Formal charge

0

Molecular weight

354.408 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N=C(N)c1ccc(cc1)c1ccc2nc([NH]c2c1)c1ccc(cc1)C(=N)N
SMILES CACTVS 3.385 NC(=N)c1ccc(cc1)c2ccc3nc([nH]c3c2)c4ccc(cc4)C(N)=N
SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1c2ccc3c(c2)[nH]c(n3)c4ccc(cc4)C(=N)N)C(=N)N
Canonical SMILES CACTVS 3.385 NC(=N)c1ccc(cc1)c2ccc3nc([nH]c3c2)c4ccc(cc4)C(N)=N
Canonical SMILES OpenEye OEToolkits 2.0.7 [H]/N=C(/c1ccc(cc1)c2ccc3c(c2)[nH]c(n3)c4ccc(cc4)/C(=N\[H])/N)\N

IUPAC InChI

InChI=1S/C21H18N6/c22-19(23)13-3-1-12(2-4-13)16-9-10-17-18(11-16)27-21(26-17)15-7-5-14(6-8-15)20(24)25/h1-11H,(H3,22,23)(H3,24,25)(H,26,27)

IUPAC InChI key

PHJDIHHRXDMKMB-UHFFFAOYSA-N
WFB

wwPDB Information

Atom count

45 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-09-06

Last modified at

2023-02-17

Status

Released

Obsoleted

Not Assigned



WFB : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 4.723 1.233 0.007
2 C14 C C2 N Y N 0 -6.405 -0.459 -0.002
3 C5 C C3 N Y N 0 3.713 0.27 0.007
4 C6 C C4 N Y N 0 2.291 0.687 0.004
5 C11 C C5 N Y N 0 -3.686 0.09 -0.001
6 C7 C C6 N Y N 0 1.964 2.047 0.002
7 C8 C C7 N Y N 0 0.66 2.446 0.0
8 C9 C C8 N Y N 0 -0.365 1.492 0.001
9 C10 C C9 N Y N 0 -2.237 0.383 0.0
10 C12 C C10 N Y N 0 -4.131 -1.233 0.007
11 C13 C C11 N Y N 0 -5.481 -1.506 0.006
12 N1 N N1 N N N 0 8.791 0.024 -0.005
13 N2 N N2 N N N 0 8.101 -2.194 -0.009
14 C3 C C12 N Y N 0 6.044 0.846 0.003
15 N3 N N3 N Y N 0 -1.711 1.584 -0.001
16 C1 C C13 N N N 0 7.793 -0.928 -0.005
17 C15 C C14 N N N 0 -7.855 -0.752 -0.002
18 C16 C C15 N Y N 0 -5.96 0.864 -0.004
19 C17 C C16 N Y N 0 -4.611 1.137 -0.004
20 C18 C C17 N Y N 0 -0.041 0.122 0.002
21 C19 C C18 N Y N 0 1.286 -0.275 -0.002
22 C2 C C19 N Y N 0 6.374 -0.511 -0.002
23 C20 C C20 N Y N 0 4.042 -1.086 0.008
24 C21 C C21 N Y N 0 5.363 -1.474 -0.002
25 N4 N N4 N N N 0 -8.767 0.281 -0.01
26 N5 N N5 N N N 0 -8.27 -1.987 0.005
27 N6 N N6 N Y N 0 -1.243 -0.558 0.002
28 H6 H H1 N N N 0 4.468 2.282 0.006
29 H7 H H2 N N N 0 2.75 2.788 0.002
30 H8 H H3 N N N 0 0.418 3.499 -0.001
31 H9 H H4 N N N 0 -3.417 -2.043 0.008
32 H10 H H5 N N N 0 -5.825 -2.529 0.012
33 H1 H H6 N N N 0 9.721 -0.25 -0.007
34 H2 H H7 N N N 0 8.562 0.966 -0.002
35 H4 H H8 N N N 0 7.399 -2.863 -0.009
36 H5 H H9 N N N 0 6.826 1.591 0.003
37 H15 H H11 N N N 0 -6.675 1.674 -0.006
38 H16 H H12 N N N 0 -4.267 2.161 -0.009
39 H18 H H13 N N N 0 1.539 -1.325 -0.005
40 H19 H H14 N N N 0 3.261 -1.832 0.008
41 H20 H H15 N N N 0 5.618 -2.524 -0.006
42 H11 H H16 N N N 0 -8.458 1.2 -0.015
43 H12 H H17 N N N 0 -9.718 0.089 -0.01
44 H13 H H18 N N N 0 -9.221 -2.179 0.005
45 H17 H H19 N N N 0 -1.361 -1.521 0.002



WFB : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2 C1 N C doub 1.3 N N
2 N1 C1 N C sing 1.38 N N
3 C1 C2 C C sing 1.48 N N
4 C2 C21 C C doub 1.4 N Y
5 C2 C3 C C sing 1.4 N Y
6 C21 C20 C C sing 1.38 N Y
7 C3 C4 C C doub 1.38 N Y
8 C20 C5 C C doub 1.4 N Y
9 C4 C5 C C sing 1.4 N Y
10 C5 C6 C C sing 1.48 N N
11 C6 C7 C C doub 1.4 N Y
12 C6 C19 C C sing 1.39 N Y
13 C7 C8 C C sing 1.36 N Y
14 C19 C18 C C doub 1.39 N Y
15 C8 C9 C C doub 1.4 N Y
16 C18 C9 C C sing 1.41 N Y
17 C18 N6 C N sing 1.38 N Y
18 C9 N3 C N sing 1.35 N Y
19 N6 C10 N C sing 1.37 N Y
20 N3 C10 N C doub 1.31 N Y
21 C10 C11 C C sing 1.48 N N
22 C11 C17 C C doub 1.4 N Y
23 C11 C12 C C sing 1.4 N Y
24 C17 C16 C C sing 1.38 N Y
25 C12 C13 C C doub 1.38 N Y
26 C16 C14 C C doub 1.4 N Y
27 C13 C14 C C sing 1.4 N Y
28 C14 C15 C C sing 1.48 N N
29 C15 N5 C N doub 1.3 N N
30 C15 N4 C N sing 1.38 N N
31 C4 H6 C H sing 1.08 N N
32 C7 H7 C H sing 1.08 N N
33 C8 H8 C H sing 1.08 N N
34 C12 H9 C H sing 1.08 N N
35 C13 H10 C H sing 1.08 N N
36 N1 H1 N H sing 0.97 N N
37 N1 H2 N H sing 0.97 N N
38 N2 H4 N H sing 0.97 N N
39 C3 H5 C H sing 1.08 N N
40 C16 H15 C H sing 1.08 N N
41 C17 H16 C H sing 1.08 N N
42 C19 H18 C H sing 1.08 N N
43 C20 H19 C H sing 1.08 N N
44 C21 H20 C H sing 1.08 N N
45 N4 H11 N H sing 0.97 N N
46 N4 H12 N H sing 0.97 N N
47 N5 H13 N H sing 0.97 N N
48 N6 H17 N H sing 0.97 N N



WFB : Used in PDB Entries

Total Number of PDB Entries: 8
Ligand Code PDB Entry ID Type Total Distinct
WFB 8ec1 Open in New Window Bound ligand 1 1
WFB 8ed6 Open in New Window Bound ligand 1 1
WFB 8eda Open in New Window Bound ligand 1 1
WFB 8f1s Open in New Window Bound ligand 1 1
WFB 8f1v Open in New Window Bound ligand 1 1
WFB 8fb4 Open in New Window Bound ligand 2 1
WFB 8fdq Open in New Window Bound ligand 1 1
WFB 8fdr Open in New Window Bound ligand 1 1