Chemical Components in the PDB

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656 : Summary

Code

656

One-letter code

X

Molecule name

2-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}-6-ISOBUTOXYBENZENOLATE

Systematic names

ProgramVersionName
ACDLabs 10.04 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-6-(2-methylpropoxy)phenolate
OpenEye OEToolkits 1.5.0 2-[5-(amino-azaniumylidene-methyl)-1H-benzimidazol-2-yl]-6-(2-methylpropoxy)phenolate

Formula

C18 H20 N4 O2

Formal charge

0

Molecular weight

324.377 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 [O-]c3c(OCC(C)C)cccc3c2nc1cc(ccc1n2)\C(=[NH2+])N
SMILES CACTVS 3.341 CC(C)COc1cccc(c1[O-])c2[nH]c3ccc(cc3n2)C(N)=[NH2+]
SMILES OpenEye OEToolkits 1.5.0 CC(C)COc1cccc(c1[O-])c2[nH]c3ccc(cc3n2)C(=[NH2+])N
Canonical SMILES CACTVS 3.341 CC(C)COc1cccc(c1[O-])c2[nH]c3ccc(cc3n2)C(N)=[NH2+]
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)COc1cccc(c1[O-])c2[nH]c3ccc(cc3n2)C(=[NH2+])N

IUPAC InChI

InChI=1S/C18H20N4O2/c1-10(2)9-24-15-5-3-4-12(16(15)23)18-21-13-7-6-11(17(19)20)8-14(13)22-18/h3-8,10,23H,9H2,1-2H3,(H3,19,20)(H,21,22)

IUPAC InChI key

HSHVHNIOQTZSOQ-UHFFFAOYSA-N
656

wwPDB Information

Atom count

44 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-03-14

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



656 : Atoms of Molecule

Total Number of Atoms: 44
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 4.929 -0.413 0.027
2 C2 C C2 N Y N 0 5.06 0.815 0.689
3 C3 C C3 N Y N 0 3.967 1.602 0.91
4 C4 C C4 N Y N 0 2.711 1.191 0.478
5 C5 C C5 N Y N 0 2.561 -0.04 -0.188
6 C6 C C6 N Y N 0 3.681 -0.841 -0.412
7 C7 C C7 N N N 0 6.121 -1.255 -0.205
8 N1 N N1 N N N 0 7.318 -0.846 0.214
9 N2 N N2 N N N 1 5.999 -2.423 -0.834
10 N3 N N3 N Y N 0 1.451 1.746 0.549
11 N4 N N4 N Y N 0 1.244 -0.178 -0.482
12 C8 C C8 N Y N 0 0.587 0.872 -0.055
13 C1' C C1' N Y N 0 -0.869 1.08 -0.199
14 C2' C C2' N Y N 0 -1.37 2.345 -0.513
15 C3' C C3' N Y N 0 -2.729 2.535 -0.646
16 C4' C C4' N Y N 0 -3.603 1.476 -0.471
17 O5' O O5' N N N 0 -3.985 -0.821 0.01
18 C5' C C5' N Y N 0 -3.12 0.215 -0.16
19 C6' C C6' N Y N 0 -1.753 0.01 -0.017
20 O6' O O6' N N N -1 -1.276 -1.225 0.288
21 C10 C C10 N N N 0 -5.3 -0.3 -0.194
22 C20 C C20 N N N 0 -6.326 -1.421 -0.015
23 C30 C C30 N N N 0 -6.303 -1.907 1.435
24 C40 C C40 N N N 0 -7.721 -0.893 -0.355
25 HC2 H HC2 N N N 0 6.033 1.14 1.027
26 HC3 H HC3 N N N 0 4.078 2.547 1.42
27 HC6 H HC6 N N N 0 3.58 -1.787 -0.923
28 HH11 H HH11 N N N 0 7.407 0.004 0.672
29 HH12 H HH12 N N N 0 8.1 -1.399 0.062
30 HH21 H HH21 N N N 0 6.782 -2.976 -0.987
31 HH22 H HH22 N N N 0 5.128 -2.72 -1.14
32 HN3 H HN3 N N N 0 1.219 2.598 0.952
33 HC2' H HC2' N N N 0 -0.692 3.174 -0.651
34 HC3' H HC3' N N N 0 -3.113 3.515 -0.889
35 HC4' H HC4' N N N 0 -4.666 1.633 -0.577
36 H10A H H10A N N N 0 -5.377 0.107 -1.202
37 H10B H H10B N N N 0 -5.494 0.489 0.533
38 H20 H H20 N N N 0 -6.078 -2.249 -0.68
39 H30A H H30A N N N 0 -6.55 -1.079 2.1
40 H30B H H30B N N N 0 -7.034 -2.706 1.562
41 H30C H H30C N N N 0 -5.309 -2.283 1.677
42 H40A H H40A N N N 0 -7.968 -0.066 0.31
43 H40B H H40B N N N 0 -7.737 -0.547 -1.388
44 H40C H H40C N N N 0 -8.452 -1.692 -0.228



656 : Chemical Bonds

Total Number of Bonds: 46
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.4 N Y
2 C1 C6 C C sing 1.39 N Y
3 C1 C7 C C sing 1.48 N N
4 C2 C3 C C sing 1.36 N Y
5 C2 HC2 C H sing 1.08 N N
6 C3 C4 C C doub 1.39 N Y
7 C3 HC3 C H sing 1.08 N N
8 C4 C5 C C sing 1.41 N Y
9 C4 N3 C N sing 1.38 N Y
10 C5 C6 C C doub 1.4 N Y
11 C5 N4 C N sing 1.36 N Y
12 C6 HC6 C H sing 1.08 N N
13 C7 N1 C N sing 1.33 N N
14 C7 N2 C N doub 1.33 N N
15 N1 HH11 N H sing 0.97 N N
16 N1 HH12 N H sing 0.97 N N
17 N2 HH21 N H sing 0.97 N N
18 N2 HH22 N H sing 0.97 N N
19 N3 C8 N C sing 1.37 N Y
20 N3 HN3 N H sing 0.97 N N
21 N4 C8 N C doub 1.31 N Y
22 C8 C1' C C sing 1.48 N Y
23 C1' C2' C C doub 1.4 N Y
24 C1' C6' C C sing 1.4 N Y
25 C2' C3' C C sing 1.38 N Y
26 C2' HC2' C H sing 1.08 N N
27 C3' C4' C C doub 1.38 N Y
28 C3' HC3' C H sing 1.08 N N
29 C4' C5' C C sing 1.39 N Y
30 C4' HC4' C H sing 1.08 N N
31 C5' C6' C C doub 1.39 N Y
32 C5' O5' C O sing 1.36 N N
33 C6' O6' C O sing 1.36 N N
34 O5' C10 O C sing 1.43 N N
35 C10 C20 C C sing 1.53 N N
36 C10 H10A C H sing 1.09 N N
37 C10 H10B C H sing 1.09 N N
38 C20 C30 C C sing 1.53 N N
39 C20 C40 C C sing 1.53 N N
40 C20 H20 C H sing 1.09 N N
41 C30 H30A C H sing 1.09 N N
42 C30 H30B C H sing 1.09 N N
43 C30 H30C C H sing 1.09 N N
44 C40 H40A C H sing 1.09 N N
45 C40 H40B C H sing 1.09 N N
46 C40 H40C C H sing 1.09 N N



656 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
656 1o2j Open in New Window Bound ligand 1 1
656 1o2k Open in New Window Bound ligand 1 1