Chemical Components in the PDB

pdbe.org/chem
spacer

1KO : Summary

Code

1KO

One-letter code

X

Molecule name

2-(4-chlorophenyl)-8-[(3S)-piperidin-3-ylamino]imidazo[1,2-c]pyrimidine-5-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 2-(4-chlorophenyl)-8-[(3S)-piperidin-3-ylamino]imidazo[1,2-c]pyrimidine-5-carboxamide
OpenEye OEToolkits 1.7.6 2-(4-chlorophenyl)-8-[[(3S)-piperidin-3-yl]amino]imidazo[1,2-c]pyrimidine-5-carboxamide

Formula

C18 H19 Cl N6 O

Formal charge

0

Molecular weight

370.836 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Clc4ccc(c1nc2c(cnc(C(=O)N)n2c1)NC3CCCNC3)cc4
SMILES CACTVS 3.370 NC(=O)c1ncc(N[CH]2CCCNC2)c3nc(cn13)c4ccc(Cl)cc4
SMILES OpenEye OEToolkits 1.7.6 c1cc(ccc1c2cn3c(n2)c(cnc3C(=O)N)NC4CCCNC4)Cl
Canonical SMILES CACTVS 3.370 NC(=O)c1ncc(N[C@H]2CCCNC2)c3nc(cn13)c4ccc(Cl)cc4
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cc(ccc1c2cn3c(n2)c(cnc3C(=O)N)N[C@H]4CCCNC4)Cl

IUPAC InChI

InChI=1S/C18H19ClN6O/c19-12-5-3-11(4-6-12)15-10-25-17(24-15)14(9-22-18(25)16(20)26)23-13-2-1-7-21-8-13/h3-6,9-10,13,21,23H,1-2,7-8H2,(H2,20,26)/t13-/m0/s1

IUPAC InChI key

VUQDZGWRLHHYTB-ZDUSSCGKSA-N
1KO

wwPDB Information

Atom count

45 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-03-11

Last modified at

2013-04-12

Status

Released

Obsoleted

Not Assigned



1KO : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C02 N Y N 0 1.542 0.239 -0.046
2 C03 C C03 N Y N 0 1.206 1.563 -0.021
3 C05 C C05 N Y N 0 -0.621 0.342 -0.121
4 C06 C C06 N Y N 0 -1.041 2.679 -0.071
5 C08 C C08 N Y N 0 -2.852 1.248 -0.176
6 C09 C C09 N Y N 0 -2.023 0.138 -0.177
7 C11 C C11 N Y N 0 2.921 -0.309 -0.011
8 C12 C C12 N N N 0 -0.534 4.059 -0.014
9 C13 C C13 S N N 0 -4.004 -1.334 -0.289
10 C14 C C14 N N N 0 -4.577 -1.321 1.13
11 C16 C C16 N N N 0 -6.353 -2.84 0.488
12 C17 C C17 N N N 0 -5.832 -2.898 -0.95
13 C18 C C18 N N N 0 -4.317 -2.68 -0.949
14 C19 C C19 N Y N 0 4.014 0.552 0.059
15 C20 C C20 N Y N 0 5.293 0.037 0.097
16 C21 C C21 N Y N 0 5.492 -1.332 0.066
17 C22 C C22 N Y N 0 4.409 -2.192 -0.0040
18 C23 C C23 N Y N 0 3.126 -1.687 -0.042
19 CL CL CL24 N N N 0 7.104 -1.974 0.114
20 H1 H H1 N N N 0 1.89 2.398 0.027
21 H10 H H10 N N N 0 -7.434 -2.98 0.488
22 H11 H H11 N N N 0 -6.059 -3.874 -1.38
23 H12 H H12 N N N 0 -6.312 -2.119 -1.543
24 H13 H H13 N N N 0 -3.948 -2.677 -1.974
25 H14 H H14 N N N 0 -3.834 -3.48 -0.389
26 H15 H H15 N N N 0 3.86 1.621 0.083
27 H16 H H16 N N N 0 6.141 0.704 0.15
28 H17 H H17 N N N 0 4.569 -3.26 -0.028
29 H18 H H18 N N N 0 2.281 -2.359 -0.091
30 H19 H H19 N N N 0 -2.351 4.93 -0.056
31 H2 H H2 N N N 0 -3.923 1.118 -0.218
32 H20 H H20 N N N 0 -1.062 6.005 0.021
33 H3 H H3 N N N 0 -1.962 -1.912 -0.232
34 H4 H H4 N N N 0 -4.454 -0.53 -0.872
35 H5 H H5 N N N 0 -4.116 -2.116 1.715
36 H6 H H6 N N N 0 -4.369 -0.358 1.597
37 H7 H H7 N N N 0 -6.445 -1.434 1.988
38 H9 H H9 N N N 0 -5.884 -3.628 1.076
39 N01 N N01 N Y N 0 0.412 -0.479 -0.106
40 N04 N N04 N Y N 0 -0.15 1.632 -0.068
41 N07 N N07 N Y N 0 -2.338 2.469 -0.123
42 N10 N N10 N N N 0 -2.552 -1.143 -0.232
43 N15 N N15 N N N 0 -6.03 -1.533 1.074
44 N25 N N25 N N N 0 -1.396 5.095 -0.016
45 O26 O O26 N N N 0 0.664 4.266 0.035



1KO : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CL C21 CL C sing 1.74 N N
2 C20 C21 C C doub 1.38 N Y
3 C20 C19 C C sing 1.38 N Y
4 C21 C22 C C sing 1.38 N Y
5 C19 C11 C C doub 1.39 N Y
6 O26 C12 O C doub 1.22 N N
7 C22 C23 C C doub 1.38 N Y
8 C11 C23 C C sing 1.39 N Y
9 C11 C02 C C sing 1.48 N N
10 C03 C02 C C doub 1.37 N Y
11 C03 N04 C N sing 1.36 N Y
12 C12 N25 C N sing 1.35 N N
13 C12 C06 C C sing 1.47 N N
14 C02 N01 C N sing 1.34 N Y
15 N04 C06 N C sing 1.37 N Y
16 N04 C05 N C sing 1.37 N Y
17 C06 N07 C N doub 1.31 N Y
18 N01 C05 N C doub 1.32 N Y
19 C05 C09 C C sing 1.42 N Y
20 N07 C08 N C sing 1.33 N Y
21 C09 C08 C C doub 1.39 N Y
22 C09 N10 C N sing 1.39 N N
23 N10 C13 N C sing 1.47 N N
24 C13 C18 C C sing 1.53 N N
25 C13 C14 C C sing 1.53 N N
26 C18 C17 C C sing 1.53 N N
27 C14 N15 C N sing 1.47 N N
28 C17 C16 C C sing 1.53 N N
29 N15 C16 N C sing 1.47 N N
30 C03 H1 C H sing 1.08 N N
31 C08 H2 C H sing 1.08 N N
32 N10 H3 N H sing 0.97 N N
33 C13 H4 C H sing 1.09 N N
34 C14 H5 C H sing 1.09 N N
35 C14 H6 C H sing 1.09 N N
36 N15 H7 N H sing 1.01 N N
37 C16 H9 C H sing 1.09 N N
38 C16 H10 C H sing 1.09 N N
39 C17 H11 C H sing 1.09 N N
40 C17 H12 C H sing 1.09 N N
41 C18 H13 C H sing 1.09 N N
42 C18 H14 C H sing 1.09 N N
43 C19 H15 C H sing 1.08 N N
44 C20 H16 C H sing 1.08 N N
45 C22 H17 C H sing 1.08 N N
46 C23 H18 C H sing 1.08 N N
47 N25 H19 N H sing 0.97 N N
48 N25 H20 N H sing 0.97 N N



1KO : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1KO 4jik Open in New Window Bound ligand 1 1