Chemical Components in the PDB

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KMA : Summary

Code

KMA

One-letter code

X

Molecule name

6-[2-(3-fluoro-5-{2-[(2R)-pyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 6-[2-(3-fluoro-5-{2-[(2R)-pyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
OpenEye OEToolkits 2.0.6 6-[2-[3-fluoranyl-5-[2-[(2~{R})-pyrrolidin-2-yl]ethyl]phenyl]ethyl]-4-methyl-pyridin-2-amine

Formula

C20 H26 F N3

Formal charge

0

Molecular weight

327.439 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Fc1cc(cc(c1)CCC2CCCN2)CCc3cc(cc(n3)N)C
SMILES CACTVS 3.385 Cc1cc(N)nc(CCc2cc(F)cc(CC[CH]3CCCN3)c2)c1
SMILES OpenEye OEToolkits 2.0.6 Cc1cc(nc(c1)N)CCc2cc(cc(c2)F)CCC3CCCN3
Canonical SMILES CACTVS 3.385 Cc1cc(N)nc(CCc2cc(F)cc(CC[C@@H]3CCCN3)c2)c1
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1cc(nc(c1)N)CCc2cc(cc(c2)F)CC[C@@H]3CCCN3

IUPAC InChI

InChI=1S/C20H26FN3/c1-14-9-19(24-20(22)10-14)7-5-16-11-15(12-17(21)13-16)4-6-18-3-2-8-23-18/h9-13,18,23H,2-8H2,1H3,(H2,22,24)/t18-/m0/s1

IUPAC InChI key

PTOVOAJZRWYLQM-SFHVURJKSA-N
KMA

wwPDB Information

Atom count

50 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-01-03

Last modified at

2019-03-08

Status

Released

Obsoleted

Not Assigned



KMA : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C17 N Y N 0 -5.579 -0.252 -0.928
2 C03 C C18 N Y N 0 -6.008 -1.452 -0.37
3 C04 C C19 N Y N 0 -5.223 -2.067 0.589
4 C05 C C16 N Y N 0 -4.028 -1.462 0.955
5 C06 C C15 N Y N 0 -3.661 -0.273 0.356
6 C07 C C20 N N N 0 -5.655 -3.365 1.221
7 C08 C C14 N N N 0 -2.365 0.389 0.749
8 C09 C C13 N N N 0 -1.514 0.625 -0.5
9 C11 C C12 N Y N 0 -0.218 1.287 -0.107
10 C12 C C2 N Y N 0 -0.128 2.665 -0.078
11 C13 C C1 N Y N 0 1.062 3.273 0.284
12 C14 C C3 N Y N 0 2.162 2.499 0.611
13 C15 C C4 N Y N 0 2.071 1.12 0.577
14 C16 C C11 N Y N 0 0.882 0.515 0.215
15 C17 C C5 N N N 0 3.27 0.277 0.928
16 C18 C C6 N N N 0 4.089 0.0040 -0.335
17 C22 C C7 R N N 0 5.306 -0.852 0.021
18 C23 C C8 N N N 0 6.215 -1.036 -1.213
19 C24 C C9 N N N 0 6.738 -2.484 -1.113
20 C25 C C10 N N N 0 6.101 -3.053 0.173
21 F13 F F1 N N N 0 1.152 4.621 0.312
22 H1 H H1 N N N 0 -0.985 3.269 -0.338
23 H10 H H10 N N N 0 6.42 -3.062 -1.981
24 H11 H H11 N N N 0 7.825 -2.489 -1.034
25 H12 H H12 N N N 0 5.833 -4.1 0.033
26 H13 H H13 N N N 0 6.784 -2.943 1.015
27 H14 H H14 N N N 0 4.128 -2.542 -0.208
28 H16 H H16 N N N 0 0.812 -0.563 0.189
29 H17 H H17 N N N 0 -2.056 1.269 -1.193
30 H18 H H18 N N N 0 -1.303 -0.33 -0.982
31 H19 H H19 N N N 0 -1.824 -0.255 1.441
32 H2 H H2 N N N 0 3.091 2.972 0.893
33 H20 H H20 N N N 0 -2.577 1.344 1.23
34 H21 H H21 N N N 0 -3.392 -1.916 1.699
35 H22 H H22 N N N 0 -6.066 1.217 -2.28
36 H23 H H23 N N N 0 -7.202 -0.016 -2.166
37 H24 H H24 N N N 0 -6.944 -1.895 -0.678
38 H25 H H25 N N N 0 -6.248 -3.156 2.111
39 H26 H H26 N N N 0 -6.253 -3.934 0.51
40 H27 H H27 N N N 0 -4.774 -3.943 1.5
41 H3 H H3 N N N 0 3.887 0.807 1.654
42 H4 H H4 N N N 0 2.936 -0.668 1.356
43 H5 H H5 N N N 0 3.472 -0.525 -1.061
44 H6 H H6 N N N 0 4.423 0.95 -0.763
45 H7 H H7 N N N 0 5.864 -0.396 0.839
46 H8 H H8 N N N 0 5.64 -0.903 -2.13
47 H9 H H9 N N N 0 7.044 -0.329 -1.181
48 N01 N N2 N Y N 0 -4.432 0.294 -0.552
49 N02 N N3 N N N 0 -6.361 0.38 -1.888
50 N21 N N1 N N N 0 4.883 -2.229 0.383



KMA : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C25 N21 C N sing 1.49 N N
2 C25 C24 C C sing 1.54 N N
3 N21 C22 N C sing 1.49 N N
4 C24 C23 C C sing 1.54 N N
5 C22 C23 C C sing 1.54 N N
6 C22 C18 C C sing 1.53 N N
7 C18 C17 C C sing 1.53 N N
8 C17 C15 C C sing 1.51 N N
9 C15 C16 C C doub 1.38 N Y
10 C15 C14 C C sing 1.38 N Y
11 C16 C11 C C sing 1.38 N Y
12 C08 C06 C C sing 1.51 N N
13 C08 C09 C C sing 1.53 N N
14 C14 C13 C C doub 1.38 N Y
15 N02 C02 N C sing 1.39 N N
16 N01 C06 N C doub 1.32 N Y
17 N01 C02 N C sing 1.32 N Y
18 C06 C05 C C sing 1.38 N Y
19 C02 C03 C C doub 1.39 N Y
20 C11 C09 C C sing 1.51 N N
21 C11 C12 C C doub 1.38 N Y
22 C13 C12 C C sing 1.38 N Y
23 C13 F13 C F sing 1.35 N N
24 C05 C04 C C doub 1.39 N Y
25 C03 C04 C C sing 1.38 N Y
26 C04 C07 C C sing 1.51 N N
27 C12 H1 C H sing 1.08 N N
28 C14 H2 C H sing 1.08 N N
29 C17 H3 C H sing 1.09 N N
30 C17 H4 C H sing 1.09 N N
31 C18 H5 C H sing 1.09 N N
32 C18 H6 C H sing 1.09 N N
33 C22 H7 C H sing 1.09 N N
34 C23 H8 C H sing 1.09 N N
35 C23 H9 C H sing 1.09 N N
36 C24 H10 C H sing 1.09 N N
37 C24 H11 C H sing 1.09 N N
38 C25 H12 C H sing 1.09 N N
39 C25 H13 C H sing 1.09 N N
40 N21 H14 N H sing 1.01 N N
41 C16 H16 C H sing 1.08 N N
42 C09 H17 C H sing 1.09 N N
43 C09 H18 C H sing 1.09 N N
44 C08 H19 C H sing 1.09 N N
45 C08 H20 C H sing 1.09 N N
46 C05 H21 C H sing 1.08 N N
47 N02 H22 N H sing 0.97 N N
48 N02 H23 N H sing 0.97 N N
49 C03 H24 C H sing 1.08 N N
50 C07 H25 C H sing 1.09 N N
51 C07 H26 C H sing 1.09 N N
52 C07 H27 C H sing 1.09 N N



KMA : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
KMA 6ng4 Open in New Window Bound ligand 2 1
KMA 6ngl Open in New Window Bound ligand 2 1
KMA 6nh2 Open in New Window Bound ligand 6 1