Chemical Components in the PDB

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MBB : Summary

Code

MBB

One-letter code

X

Molecule name

2'-(3-METHYL-4-DIMETHYLAMINOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE

Systematic names

ProgramVersionName
ACDLabs 10.04 N,N,3-trimethyl-4-[5-(4-methylpiperazin-1-yl)-1H,1'H-2,5'-bibenzimidazol-2'-yl]aniline
OpenEye OEToolkits 1.5.0 N,N,3-trimethyl-4-[5-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-benzimidazol-2-yl]aniline

Formula

C28 H31 N7

Formal charge

0

Molecular weight

465.593 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 n2c(c1ccc(N(C)C)cc1C)nc3ccc(cc23)c5nc4cc(ccc4n5)N6CCN(C)CC6
SMILES CACTVS 3.341 CN1CCN(CC1)c2ccc3[nH]c(nc3c2)c4ccc5[nH]c(nc5c4)c6ccc(cc6C)N(C)C
SMILES OpenEye OEToolkits 1.5.0 Cc1cc(ccc1c2[nH]c3ccc(cc3n2)c4[nH]c5ccc(cc5n4)N6CCN(CC6)C)N(C)C
Canonical SMILES CACTVS 3.341 CN1CCN(CC1)c2ccc3[nH]c(nc3c2)c4ccc5[nH]c(nc5c4)c6ccc(cc6C)N(C)C
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1cc(ccc1c2[nH]c3ccc(cc3n2)c4[nH]c5ccc(cc5n4)N6CCN(CC6)C)N(C)C

IUPAC InChI

InChI=1S/C28H31N7/c1-18-15-20(33(2)3)6-8-22(18)28-30-23-9-5-19(16-25(23)32-28)27-29-24-10-7-21(17-26(24)31-27)35-13-11-34(4)12-14-35/h5-10,15-17H,11-14H2,1-4H3,(H,29,31)(H,30,32)

IUPAC InChI key

ADKLMOJIJGHCCD-UHFFFAOYSA-N
MBB

wwPDB Information

Atom count

66 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



MBB : Atoms of Molecule

Total Number of Atoms: 66
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N Y N 0 0.98 0.113 -8.32
2 C1 C C1 N Y N 0 0.002 0.182 -5.728
3 C2 C C2 N Y N 0 0.154 1.157 -7.917
4 C3 C C3 N Y N 0 -0.333 1.194 -6.63
5 C4 C C4 N Y N 0 1.316 -0.896 -7.424
6 C5 C C5 N Y N 0 0.836 -0.861 -6.133
7 N N N N N N 0 1.471 0.078 -9.623
8 C6 C C6 N Y N 0 -0.517 0.22 -4.346
9 C7 C C7 N Y N 0 -0.616 0.047 -2.175
10 C8 C C8 N Y N 0 -1.875 0.493 -2.618
11 C9 C C9 N Y N 0 -2.891 0.734 -1.702
12 C10 C C10 N Y N 0 -2.673 0.538 -0.368
13 C11 C C11 N Y N 0 -1.427 0.095 0.09
14 C12 C C12 N Y N 0 -0.395 -0.145 -0.81
15 N1 N N1 N Y N 0 0.165 -0.1 -3.274
16 N2 N N2 N Y N 0 -1.786 0.594 -3.992
17 C13 C C13 N Y N 0 -1.205 -0.112 1.537
18 C14 C C14 N Y N 0 -0.243 -0.123 3.493
19 C15 C C15 N Y N 0 -1.524 -0.679 3.654
20 C16 C C16 N Y N 0 -1.943 -1.108 4.905
21 C17 C C17 N Y N 0 -1.102 -0.988 5.991
22 C18 C C18 N Y N 0 0.169 -0.439 5.84
23 N3 N N3 N Y N 0 -0.109 0.201 2.183
24 N4 N N4 N Y N 0 -2.112 -0.66 2.401
25 C19 C C19 N Y N 0 0.599 -0.002 4.602
26 N5 N N5 N N N 0 1.012 -0.324 6.951
27 N6 N N6 N N N 0 1.271 0.779 9.621
28 C20 C C20 N N N 0 0.274 -0.862 8.1
29 C21 C C21 N N N 0 1.089 -0.657 9.377
30 C22 C C22 N N N 0 2.009 1.317 8.472
31 C23 C C23 N N N 0 1.194 1.111 7.195
32 C24 C C24 N N N 0 2.156 0.9 10.787
33 CN1 C CN1 N N N 0 2.437 -0.951 -10.015
34 CN2 C CN2 N N N 0 1.022 1.071 -10.602
35 C25 C C25 N N N 0 1.201 -1.955 -5.163
36 H2 H H2 N N N 0 -0.105 1.939 -8.615
37 H3 H H3 N N N 0 -0.975 2.005 -6.318
38 H4 H H4 N N N 0 1.957 -1.706 -7.74
39 H9 H H9 N N N 0 -3.857 1.075 -2.045
40 H10 H H10 N N N 0 -3.468 0.727 0.338
41 H12 H H12 N N N 0 0.567 -0.481 -0.457
42 HN2 H HN2 N N N 0 -2.491 0.877 -4.595
43 H16 H H16 N N N 0 -2.927 -1.535 5.028
44 H17 H H17 N N N 0 -1.431 -1.323 6.964
45 HN4 H HN4 N N N 0 -3.002 -0.977 2.178
46 H19 H H19 N N N 0 1.584 0.427 4.491
47 H201 H 1H20 N N N 0 0.095 -1.926 7.95
48 H202 H 2H20 N N N 0 -0.68 -0.344 8.192
49 H211 H 1H21 N N N 0 2.063 -1.132 9.265
50 H212 H 2H21 N N N 0 0.562 -1.104 10.219
51 H221 H 1H22 N N N 0 2.188 2.381 8.622
52 H222 H 2H22 N N N 0 2.964 0.799 8.38
53 H231 H 1H23 N N N 0 1.721 1.559 6.353
54 H232 H 2H23 N N N 0 0.22 1.587 7.307
55 H241 H 1H24 N N N 0 2.322 1.954 11.009
56 H242 H 2H24 N N N 0 1.693 0.415 11.647
57 HN13 H 3HN1 N N N 0 1.994 -1.937 -9.874
58 H243 H 3H24 N N N 0 3.11 0.42 10.57
59 HN11 H 1HN1 N N N 0 2.704 -0.819 -11.063
60 HN12 H 2HN1 N N N 0 3.332 -0.863 -9.398
61 HN21 H 1HN2 N N N 0 0.381 1.802 -10.11
62 HN22 H 2HN2 N N N 0 1.888 1.576 -11.031
63 HN23 H 3HN2 N N N 0 0.464 0.573 -11.395
64 H251 H 1H25 N N N 0 2.116 -1.684 -4.636
65 H252 H 2H25 N N N 0 0.393 -2.087 -4.444
66 H253 H 3H25 N N N 0 1.358 -2.886 -5.708



MBB : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C C2 C C doub 1.39 N Y
2 C C4 C C sing 1.39 N Y
3 C N C N sing 1.39 N N
4 C1 C3 C C doub 1.4 N Y
5 C1 C5 C C sing 1.4 N Y
6 C1 C6 C C sing 1.48 N Y
7 C2 C3 C C sing 1.38 N Y
8 C2 H2 C H sing 1.08 N N
9 C3 H3 C H sing 1.08 N N
10 C4 C5 C C doub 1.38 N Y
11 C4 H4 C H sing 1.08 N N
12 C5 C25 C C sing 1.51 N N
13 N CN1 N C sing 1.46 N N
14 N CN2 N C sing 1.46 N N
15 C6 N1 C N doub 1.31 N Y
16 C6 N2 C N sing 1.37 N Y
17 C7 C8 C C doub 1.41 N Y
18 C7 C12 C C sing 1.4 N Y
19 C7 N1 C N sing 1.36 N Y
20 C8 C9 C C sing 1.39 N Y
21 C8 N2 C N sing 1.38 N Y
22 C9 C10 C C doub 1.37 N Y
23 C9 H9 C H sing 1.08 N N
24 C10 C11 C C sing 1.4 N Y
25 C10 H10 C H sing 1.08 N N
26 C11 C12 C C doub 1.39 N Y
27 C11 C13 C C sing 1.48 N Y
28 C12 H12 C H sing 1.08 N N
29 N2 HN2 N H sing 0.97 N N
30 C13 N3 C N doub 1.31 N Y
31 C13 N4 C N sing 1.37 N Y
32 C14 C15 C C doub 1.41 N Y
33 C14 N3 C N sing 1.36 N Y
34 C14 C19 C C sing 1.4 N Y
35 C15 C16 C C sing 1.39 N Y
36 C15 N4 C N sing 1.38 N Y
37 C16 C17 C C doub 1.38 N Y
38 C16 H16 C H sing 1.08 N N
39 C17 C18 C C sing 1.39 N Y
40 C17 H17 C H sing 1.08 N N
41 C18 C19 C C doub 1.38 N Y
42 C18 N5 C N sing 1.4 N N
43 N4 HN4 N H sing 0.97 N N
44 C19 H19 C H sing 1.08 N N
45 N5 C20 N C sing 1.47 N N
46 N5 C23 N C sing 1.47 N N
47 N6 C21 N C sing 1.47 N N
48 N6 C22 N C sing 1.47 N N
49 N6 C24 N C sing 1.47 N N
50 C20 C21 C C sing 1.53 N N
51 C20 H201 C H sing 1.09 N N
52 C20 H202 C H sing 1.09 N N
53 C21 H211 C H sing 1.09 N N
54 C21 H212 C H sing 1.09 N N
55 C22 C23 C C sing 1.53 N N
56 C22 H221 C H sing 1.09 N N
57 C22 H222 C H sing 1.09 N N
58 C23 H231 C H sing 1.09 N N
59 C23 H232 C H sing 1.09 N N
60 C24 H241 C H sing 1.09 N N
61 C24 H242 C H sing 1.09 N N
62 C24 H243 C H sing 1.09 N N
63 CN1 HN11 C H sing 1.09 N N
64 CN1 HN12 C H sing 1.09 N N
65 CN1 HN13 C H sing 1.09 N N
66 CN2 HN21 C H sing 1.09 N N
67 CN2 HN22 C H sing 1.09 N N
68 CN2 HN23 C H sing 1.09 N N
69 C25 H251 C H sing 1.09 N N
70 C25 H252 C H sing 1.09 N N
71 C25 H253 C H sing 1.09 N N



MBB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
MBB 1qv4 Open in New Window Bound ligand 1 1