Chemical Components in the PDB

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W79 : Summary

Code

W79

One-letter code

X

Molecule name

4-methyl-6-[2-(5-{3-[(methylamino)methyl]phenyl}pyridin-3-yl)ethyl]pyridin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 4-methyl-6-[2-(5-{3-[(methylamino)methyl]phenyl}pyridin-3-yl)ethyl]pyridin-2-amine
OpenEye OEToolkits 2.0.6 4-methyl-6-[2-[5-[3-(methylaminomethyl)phenyl]pyridin-3-yl]ethyl]pyridin-2-amine

Formula

C21 H24 N4

Formal charge

0

Molecular weight

332.442 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Nc1nc(cc(c1)C)CCc2cc(cnc2)c3cccc(c3)CNC
SMILES CACTVS 3.385 CNCc1cccc(c1)c2cncc(CCc3cc(C)cc(N)n3)c2
SMILES OpenEye OEToolkits 2.0.6 Cc1cc(nc(c1)N)CCc2cc(cnc2)c3cccc(c3)CNC
Canonical SMILES CACTVS 3.385 CNCc1cccc(c1)c2cncc(CCc3cc(C)cc(N)n3)c2
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1cc(nc(c1)N)CCc2cc(cnc2)c3cccc(c3)CNC

IUPAC InChI

InChI=1S/C21H24N4/c1-15-8-20(25-21(22)9-15)7-6-17-11-19(14-24-13-17)18-5-3-4-16(10-18)12-23-2/h3-5,8-11,13-14,23H,6-7,12H2,1-2H3,(H2,22,25)

IUPAC InChI key

MGNVQSKYSZRQCR-UHFFFAOYSA-N
W79

wwPDB Information

Atom count

49 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-09-05

Last modified at

2018-07-06

Status

Released

Obsoleted

Not Assigned



W79 : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N02 N N1 N N N 0 7.034 -1.467 -0.715
2 C02 C C1 N Y N 0 6.174 -0.496 -0.217
3 C06 C C6 N Y N 0 4.054 0.096 0.478
4 C03 C C2 N Y N 0 6.652 0.787 0.031
5 C04 C C3 N Y N 0 5.783 1.745 0.521
6 C07 C C4 N N N 0 6.261 3.146 0.803
7 C05 C C5 N Y N 0 4.46 1.387 0.747
8 N01 N N2 N Y N 0 4.905 -0.798 0.011
9 C08 C C7 N N N 0 2.62 -0.299 0.721
10 C09 C C8 N N N 0 2.027 -0.883 -0.562
11 C13 C C9 N Y N 0 0.593 -1.277 -0.319
12 C14 C C10 N Y N 0 -0.429 -0.37 -0.538
13 C15 C C13 N Y N 0 -1.743 -0.781 -0.299
14 C12 C C11 N Y N 0 0.283 -2.552 0.12
15 N11 N N3 N Y N 0 -0.967 -2.911 0.336
16 C16 C C12 N Y N 0 -1.972 -2.08 0.147
17 C21 C C14 N Y N 0 -2.876 0.154 -0.512
18 C26 C C15 N Y N 0 -4.182 -0.262 -0.26
19 C22 C C16 N Y N 0 -2.637 1.452 -0.958
20 C23 C C17 N Y N 0 -3.694 2.317 -1.154
21 C24 C C18 N Y N 0 -4.989 1.898 -0.907
22 C25 C C19 N Y N 0 -5.232 0.612 -0.459
23 C27 C C20 N N N 0 -6.645 0.164 -0.187
24 N28 N N4 N N N 0 -6.99 0.454 1.211
25 C29 C C21 N N N 0 -8.363 0.03 1.513
26 H1 H H1 N N N 0 6.705 -2.362 -0.894
27 H2 H H2 N N N 0 7.964 -1.249 -0.888
28 H3 H H3 N N N 0 7.687 1.031 -0.155
29 H4 H H4 N N N 0 6.614 3.209 1.832
30 H5 H H5 N N N 0 7.075 3.396 0.123
31 H6 H H6 N N N 0 5.438 3.847 0.658
32 H7 H H7 N N N 0 3.757 2.112 1.13
33 H8 H H8 N N N 0 2.578 -1.046 1.514
34 H9 H H9 N N N 0 2.047 0.58 1.019
35 H10 H H10 N N N 0 2.069 -0.136 -1.355
36 H11 H H11 N N N 0 2.6 -1.761 -0.86
37 H12 H H12 N N N 0 -0.216 0.631 -0.885
38 H13 H H13 N N N 0 1.078 -3.264 0.288
39 H14 H H14 N N N 0 -2.983 -2.411 0.335
40 H15 H H15 N N N 0 -4.372 -1.265 0.09
41 H16 H H16 N N N 0 -1.626 1.78 -1.151
42 H17 H H17 N N N 0 -3.51 3.324 -1.5
43 H18 H H18 N N N 0 -5.813 2.579 -1.061
44 H19 H H19 N N N 0 -7.328 0.697 -0.848
45 H20 H H20 N N N 0 -6.727 -0.908 -0.367
46 H21 H H21 N N N 0 -6.331 0.023 1.843
47 H23 H H23 N N N 0 -9.059 0.562 0.864
48 H24 H H24 N N N 0 -8.458 -1.043 1.345
49 H25 H H25 N N N 0 -8.593 0.256 2.555



W79 : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C07 C04 C C sing 1.51 N N
2 C12 N11 C N doub 1.32 N Y
3 C12 C13 C C sing 1.38 N Y
4 N11 C16 N C sing 1.32 N Y
5 C04 C05 C C doub 1.39 N Y
6 C04 C03 C C sing 1.38 N Y
7 C05 C06 C C sing 1.38 N Y
8 C03 C02 C C doub 1.39 N Y
9 C09 C13 C C sing 1.51 N N
10 C09 C08 C C sing 1.53 N N
11 C13 C14 C C doub 1.38 N Y
12 C16 C15 C C doub 1.39 N Y
13 C06 C08 C C sing 1.51 N N
14 C06 N01 C N doub 1.32 N Y
15 C02 N01 C N sing 1.32 N Y
16 C02 N02 C N sing 1.39 N N
17 C15 C14 C C sing 1.4 N Y
18 C15 C21 C C sing 1.48 N N
19 C21 C22 C C doub 1.39 N Y
20 C21 C26 C C sing 1.39 N Y
21 C22 C23 C C sing 1.38 N Y
22 C26 C25 C C doub 1.38 N Y
23 C23 C24 C C doub 1.38 N Y
24 C25 C24 C C sing 1.38 N Y
25 C25 C27 C C sing 1.51 N N
26 C27 N28 C N sing 1.47 N N
27 N28 C29 N C sing 1.47 N N
28 N02 H1 N H sing 0.97 N N
29 N02 H2 N H sing 0.97 N N
30 C03 H3 C H sing 1.08 N N
31 C07 H4 C H sing 1.09 N N
32 C07 H5 C H sing 1.09 N N
33 C07 H6 C H sing 1.09 N N
34 C05 H7 C H sing 1.08 N N
35 C08 H8 C H sing 1.09 N N
36 C08 H9 C H sing 1.09 N N
37 C09 H10 C H sing 1.09 N N
38 C09 H11 C H sing 1.09 N N
39 C14 H12 C H sing 1.08 N N
40 C12 H13 C H sing 1.08 N N
41 C16 H14 C H sing 1.08 N N
42 C26 H15 C H sing 1.08 N N
43 C22 H16 C H sing 1.08 N N
44 C23 H17 C H sing 1.08 N N
45 C24 H18 C H sing 1.08 N N
46 C27 H19 C H sing 1.09 N N
47 C27 H20 C H sing 1.09 N N
48 N28 H21 N H sing 1.01 N N
49 C29 H23 C H sing 1.09 N N
50 C29 H24 C H sing 1.09 N N
51 C29 H25 C H sing 1.09 N N



W79 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
W79 6auv Open in New Window Bound ligand 2 1
W79 6av3 Open in New Window Bound ligand 2 1