Chemical Components in the PDB

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12S : Summary

Code

12S

One-letter code

X

Molecule name

6,6'-{[5-(3-aminopropyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)

Systematic names

ProgramVersionName
ACDLabs 12.01 6,6'-{[5-(3-aminopropyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)
OpenEye OEToolkits 1.7.6 6-[2-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]-5-(3-azanylpropyl)phenyl]ethyl]-4-methyl-pyridin-2-amine

Formula

C25 H33 N5

Formal charge

0

Molecular weight

403.563 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n1c(N)cc(cc1CCc2cc(cc(c2)CCCN)CCc3nc(N)cc(c3)C)C
SMILES CACTVS 3.370 Cc1cc(N)nc(CCc2cc(CCCN)cc(CCc3cc(C)cc(N)n3)c2)c1
SMILES OpenEye OEToolkits 1.7.6 Cc1cc(nc(c1)N)CCc2cc(cc(c2)CCc3cc(cc(n3)N)C)CCCN
Canonical SMILES CACTVS 3.370 Cc1cc(N)nc(CCc2cc(CCCN)cc(CCc3cc(C)cc(N)n3)c2)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1cc(nc(c1)N)CCc2cc(cc(c2)CCc3cc(cc(n3)N)C)CCCN

IUPAC InChI

InChI=1S/C25H33N5/c1-17-10-22(29-24(27)12-17)7-5-20-14-19(4-3-9-26)15-21(16-20)6-8-23-11-18(2)13-25(28)30-23/h10-16H,3-9,26H2,1-2H3,(H2,27,29)(H2,28,30)

IUPAC InChI key

TUMIYXWSFLIVFR-UHFFFAOYSA-N
12S

wwPDB Information

Atom count

63 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-01-08

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



12S : Atoms of Molecule

Total Number of Atoms: 63
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 -0.02 2.797 -0.99
2 C12 C C12 N Y N 0 4.257 -1.074 0.263
3 C13 C C13 N Y N 0 5.347 -0.586 0.957
4 C14 C C14 N Y N 0 6.546 -1.285 0.918
5 C15 C C15 N Y N 0 6.609 -2.447 0.17
6 C16 C C16 N Y N 0 5.471 -2.883 -0.5
7 C17 C C17 N N N 0 7.757 -0.778 1.658
8 C18 C C18 N N N 0 2.951 -0.324 0.307
9 C19 C C19 N N N 0 2.488 -0.023 -1.12
10 C2 C C2 N Y N 0 1.179 2.109 -1.031
11 C22 C C22 N Y N 0 -4.232 -1.096 0.413
12 C23 C C23 N Y N 0 -4.312 -2.316 1.053
13 C24 C C24 N Y N 0 -5.513 -3.011 1.045
14 C25 C C25 N Y N 0 -6.596 -2.452 0.391
15 C26 C C26 N Y N 0 -6.444 -1.218 -0.234
16 C27 C C27 N N N 0 -5.636 -4.346 1.734
17 C28 C C28 N N N 0 -2.929 -0.339 0.412
18 C29 C C29 N N N 0 -2.516 -0.035 -1.029
19 C3 C C3 N Y N 0 1.181 0.727 -1.076
20 C4 C C4 N Y N 0 -0.014 0.033 -1.076
21 C5 C C5 N Y N 0 -1.212 0.721 -1.03
22 C6 C C6 N Y N 0 -1.215 2.103 -0.989
23 C7 C C7 N N N 0 -0.023 4.303 -0.947
24 C8 C C8 N N N 0 0.0020 4.771 0.51
25 C9 C C9 N N N 0 -0.0020 6.301 0.554
26 H1 H H1 N N N 0 -8.378 -1.103 -0.92
27 H10 H H10 N N N 0 -2.394 -0.97 -1.577
28 H11 H H11 N N N 0 -3.287 0.568 -1.508
29 H12 H H12 N N N 0 -0.012 -1.046 -1.112
30 H13 H H13 N N N 0 -2.151 2.64 -0.958
31 H14 H H14 N N N 0 0.858 4.683 -1.465
32 H15 H H15 N N N 0 -0.922 4.679 -1.434
33 H16 H H16 N N N 0 -0.879 4.391 1.028
34 H17 H H17 N N N 0 0.901 4.396 0.997
35 H18 H H18 N N N 0 0.879 6.681 0.035
36 H19 H H19 N N N 0 -0.901 6.676 0.066
37 H2 H H2 N N N 0 -7.424 0.218 -1.329
38 H20 H H20 N N N 0 0.02 7.758 2.008
39 H21 H H21 N N N 0 -0.75 6.358 2.471
40 H23 H H23 N N N 0 2.113 2.651 -1.03
41 H24 H H24 N N N 0 2.352 -0.958 -1.663
42 H25 H H25 N N N 0 3.239 0.585 -1.625
43 H26 H H26 N N N 0 3.087 0.611 0.85
44 H27 H H27 N N N 0 2.2 -0.932 0.812
45 H28 H H28 N N N 0 5.267 0.329 1.524
46 H29 H H29 N N N 0 4.726 -4.362 -1.716
47 H3 H H3 N N N 0 -7.545 -2.965 0.365
48 H30 H H30 N N N 0 6.341 -4.565 -1.298
49 H31 H H31 N N N 0 7.528 -3.013 0.115
50 H32 H H32 N N N 0 8.326 -0.11 1.011
51 H33 H H33 N N N 0 7.438 -0.236 2.549
52 H34 H H34 N N N 0 8.383 -1.621 1.95
53 H4 H H4 N N N 0 -5.385 -5.142 1.032
54 H5 H H5 N N N 0 -4.952 -4.381 2.582
55 H6 H H6 N N N 0 -6.658 -4.481 2.086
56 H7 H H7 N N N 0 -3.448 -2.725 1.556
57 H8 H H8 N N N 0 -3.051 0.595 0.96
58 H9 H H9 N N N 0 -2.158 -0.943 0.891
59 N10 N N10 N N N 0 0.022 6.75 1.952
60 N11 N N11 N Y N 0 4.344 -2.191 -0.434
61 N16 N N16 N N N 0 5.518 -4.055 -1.246
62 N21 N N21 N Y N 0 -5.28 -0.588 -0.209
63 N26 N N26 N N N 0 -7.524 -0.644 -0.895



12S : Chemical Bonds

Total Number of Bonds: 65
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C17 C14 C C sing 1.51 N N
2 C14 C15 C C doub 1.38 N Y
3 C14 C13 C C sing 1.39 N Y
4 C15 C16 C C sing 1.39 N Y
5 C13 C12 C C doub 1.38 N Y
6 C16 N16 C N sing 1.39 N N
7 C16 N11 C N doub 1.32 N Y
8 C12 N11 C N sing 1.32 N Y
9 C12 C18 C C sing 1.51 N N
10 C19 C18 C C sing 1.53 N N
11 C19 C3 C C sing 1.51 N N
12 C2 C3 C C doub 1.38 N Y
13 C2 C1 C C sing 1.38 N Y
14 C7 C1 C C sing 1.51 N N
15 C7 C8 C C sing 1.53 N N
16 C3 C4 C C sing 1.38 N Y
17 C1 C6 C C doub 1.38 N Y
18 N10 C9 N C sing 1.47 N N
19 C8 C9 C C sing 1.53 N N
20 C4 C5 C C doub 1.38 N Y
21 C6 C5 C C sing 1.38 N Y
22 C5 C29 C C sing 1.51 N N
23 C29 C28 C C sing 1.53 N N
24 C28 C22 C C sing 1.51 N N
25 C22 N21 C N doub 1.32 N Y
26 C22 C23 C C sing 1.38 N Y
27 N21 C26 N C sing 1.32 N Y
28 C23 C24 C C doub 1.39 N Y
29 C26 N26 C N sing 1.39 N N
30 C26 C25 C C doub 1.39 N Y
31 C24 C25 C C sing 1.38 N Y
32 C24 C27 C C sing 1.51 N N
33 N26 H1 N H sing 0.97 N N
34 N26 H2 N H sing 0.97 N N
35 C25 H3 C H sing 1.08 N N
36 C27 H4 C H sing 1.09 N N
37 C27 H5 C H sing 1.09 N N
38 C27 H6 C H sing 1.09 N N
39 C23 H7 C H sing 1.08 N N
40 C28 H8 C H sing 1.09 N N
41 C28 H9 C H sing 1.09 N N
42 C29 H10 C H sing 1.09 N N
43 C29 H11 C H sing 1.09 N N
44 C4 H12 C H sing 1.08 N N
45 C6 H13 C H sing 1.08 N N
46 C7 H14 C H sing 1.09 N N
47 C7 H15 C H sing 1.09 N N
48 C8 H16 C H sing 1.09 N N
49 C8 H17 C H sing 1.09 N N
50 C9 H18 C H sing 1.09 N N
51 C9 H19 C H sing 1.09 N N
52 N10 H20 N H sing 1.01 N N
53 N10 H21 N H sing 1.01 N N
54 C2 H23 C H sing 1.08 N N
55 C19 H24 C H sing 1.09 N N
56 C19 H25 C H sing 1.09 N N
57 C18 H26 C H sing 1.09 N N
58 C18 H27 C H sing 1.09 N N
59 C13 H28 C H sing 1.08 N N
60 N16 H29 N H sing 0.97 N N
61 N16 H30 N H sing 0.97 N N
62 C15 H31 C H sing 1.08 N N
63 C17 H32 C H sing 1.09 N N
64 C17 H33 C H sing 1.09 N N
65 C17 H34 C H sing 1.09 N N



12S : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
12S 4ims Open in New Window Bound ligand 2 1