Chemical Components in the PDB

pdbe.org/chem
spacer

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 N26 N N26 N N N 0 -7.524 -0.644 -0.895
2 C26 C C26 N Y N 0 -6.444 -1.218 -0.234
3 C25 C C25 N Y N 0 -6.596 -2.452 0.391
4 C24 C C24 N Y N 0 -5.513 -3.011 1.045
5 C27 C C27 N N N 0 -5.636 -4.346 1.734
6 C23 C C23 N Y N 0 -4.312 -2.316 1.053
7 N21 N N21 N Y N 0 -5.28 -0.588 -0.209
8 C22 C C22 N Y N 0 -4.232 -1.096 0.413
9 C28 C C28 N N N 0 -2.929 -0.339 0.412
10 C29 C C29 N N N 0 -2.516 -0.035 -1.029
11 C5 C C5 N Y N 0 -1.212 0.721 -1.03
12 C4 C C4 N Y N 0 -0.014 0.033 -1.076
13 C6 C C6 N Y N 0 -1.215 2.103 -0.989
14 C1 C C1 N Y N 0 -0.02 2.797 -0.99
15 C7 C C7 N N N 0 -0.023 4.303 -0.947
16 C8 C C8 N N N 0 0.0020 4.771 0.51
17 C9 C C9 N N N 0 -0.0020 6.301 0.554
18 N10 N N10 N N N 0 0.022 6.75 1.952
19 C2 C C2 N Y N 0 1.179 2.109 -1.031
20 C3 C C3 N Y N 0 1.181 0.727 -1.076
21 C19 C C19 N N N 0 2.488 -0.023 -1.12
22 C18 C C18 N N N 0 2.951 -0.324 0.307
23 C12 C C12 N Y N 0 4.257 -1.074 0.263
24 C13 C C13 N Y N 0 5.347 -0.586 0.957
25 N11 N N11 N Y N 0 4.344 -2.191 -0.434
26 C16 C C16 N Y N 0 5.471 -2.883 -0.5
27 N16 N N16 N N N 0 5.518 -4.055 -1.246
28 C15 C C15 N Y N 0 6.609 -2.447 0.17
29 C14 C C14 N Y N 0 6.546 -1.285 0.918
30 C17 C C17 N N N 0 7.757 -0.778 1.658
31 H1 H H1 N N N 0 -8.378 -1.103 -0.92
32 H2 H H2 N N N 0 -7.424 0.218 -1.329
33 H3 H H3 N N N 0 -7.545 -2.965 0.365
34 H4 H H4 N N N 0 -5.385 -5.142 1.032
35 H5 H H5 N N N 0 -4.952 -4.381 2.582
36 H6 H H6 N N N 0 -6.658 -4.481 2.086
37 H7 H H7 N N N 0 -3.448 -2.725 1.556
38 H8 H H8 N N N 0 -3.051 0.595 0.96
39 H9 H H9 N N N 0 -2.158 -0.943 0.891
40 H10 H H10 N N N 0 -2.394 -0.97 -1.577
41 H11 H H11 N N N 0 -3.287 0.568 -1.508
42 H12 H H12 N N N 0 -0.012 -1.046 -1.112
43 H13 H H13 N N N 0 -2.151 2.64 -0.958
44 H14 H H14 N N N 0 0.858 4.683 -1.465
45 H15 H H15 N N N 0 -0.922 4.679 -1.434
46 H16 H H16 N N N 0 -0.879 4.391 1.028
47 H17 H H17 N N N 0 0.901 4.396 0.997
48 H18 H H18 N N N 0 0.879 6.681 0.035
49 H19 H H19 N N N 0 -0.901 6.676 0.066
50 H20 H H20 N N N 0 0.02 7.758 2.008
51 H21 H H21 N N N 0 -0.75 6.358 2.471
52 H23 H H23 N N N 0 2.113 2.651 -1.03
53 H24 H H24 N N N 0 2.352 -0.958 -1.663
54 H25 H H25 N N N 0 3.239 0.585 -1.625
55 H26 H H26 N N N 0 3.087 0.611 0.85
56 H27 H H27 N N N 0 2.2 -0.932 0.812
57 H28 H H28 N N N 0 5.267 0.329 1.524
58 H29 H H29 N N N 0 4.726 -4.362 -1.716
59 H30 H H30 N N N 0 6.341 -4.565 -1.298
60 H31 H H31 N N N 0 7.528 -3.013 0.115
61 H32 H H32 N N N 0 8.326 -0.11 1.011
62 H33 H H33 N N N 0 7.438 -0.236 2.549
63 H34 H H34 N N N 0 8.383 -1.621 1.95



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: 2
Ligand Code PDB Entry ID Type Total Distinct
12S 4d3k Open in New Window Bound ligand 2 1
12S 4ims Open in New Window Bound ligand 2 1