Chemical Components in the PDB

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3KO : Summary

Code

3KO

One-letter code

X

Molecule name

(2E,5R)-5-(2-cyclohexylethyl)-5-{[(3R)-1-(cyclopentylacetyl)pyrrolidin-3-yl]methyl}-2-imino-3-methylimidazolidin-4-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (2E,5R)-5-(2-cyclohexylethyl)-5-{[(3R)-1-(cyclopentylacetyl)pyrrolidin-3-yl]methyl}-2-imino-3-methylimidazolidin-4-one
OpenEye OEToolkits 1.7.6 (5R)-2-azanylidene-5-(2-cyclohexylethyl)-5-[[(3R)-1-(2-cyclopentylethanoyl)pyrrolidin-3-yl]methyl]-3-methyl-imidazolidin-4-one

Formula

C24 H40 N4 O2

Formal charge

0

Molecular weight

416.6 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(N3CCC(CC1(C(=O)N(C(=[N@H])N1)C)CCC2CCCCC2)C3)CC4CCCC4
SMILES CACTVS 3.385 CN1C(=N)N[C](CCC2CCCCC2)(C[CH]3CCN(C3)C(=O)CC4CCCC4)C1=O
SMILES OpenEye OEToolkits 1.7.6 CN1C(=O)C(NC1=N)(CCC2CCCCC2)CC3CCN(C3)C(=O)CC4CCCC4
Canonical SMILES CACTVS 3.385 CN1C(=N)N[C@](CCC2CCCCC2)(C[C@H]3CCN(C3)C(=O)CC4CCCC4)C1=O
Canonical SMILES OpenEye OEToolkits 1.7.6 [H]/N=C/1\N[C@](C(=O)N1C)(CCC2CCCCC2)C[C@H]3CCN(C3)C(=O)CC4CCCC4

IUPAC InChI

InChI=1S/C24H40N4O2/c1-27-22(30)24(26-23(27)25,13-11-18-7-3-2-4-8-18)16-20-12-14-28(17-20)21(29)15-19-9-5-6-10-19/h18-20H,2-17H2,1H3,(H2,25,26)/t20-,24-/m1/s1

IUPAC InChI key

ZROUWOKUKKGJPH-HYBUGGRVSA-N
3KO

wwPDB Information

Atom count

70 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-09-05

Last modified at

2020-06-27

Status

Released

Obsoleted

Not Assigned



3KO : Atoms of Molecule

Total Number of Atoms: 70
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C2 N N N 0 -1.556 1.744 1.08
2 C3 C C3 N N N 0 -1.716 1.17 -1.084
3 C4 C C4 R N N 0 -1.798 -0.092 -0.252
4 C7 C C7 N N N 0 4.317 -0.911 -0.173
5 N1 N N1 N N N 0 -1.571 2.191 -0.218
6 C9 C C9 N N N 0 -0.641 -1.036 -0.589
7 C13 C C13 N N N 0 5.361 -0.423 0.798
8 C10 C C10 N N N 0 1.886 -1.22 -0.726
9 C12 C C12 N N N 0 -3.141 -0.789 -0.477
10 C27 C C27 N N N 0 -8.101 -0.195 -0.447
11 C28 C C28 N N N 0 8.587 0.349 -1.018
12 C29 C C29 N N N 0 9.099 -0.024 0.384
13 C30 C C30 N N N 0 -8.263 -1.329 0.567
14 C26 C C26 N N N 0 -7.128 -2.34 0.388
15 C25 C C25 N N N 0 -5.785 -1.643 0.613
16 C24 C C24 N N N 0 -6.758 0.502 -0.222
17 C23 C C23 N N N 0 7.047 0.281 -0.958
18 C22 C C22 N N N 0 7.853 -0.305 1.249
19 C14 C C14 N N N 0 2.462 -0.199 1.36
20 C16 C C16 R N N 0 0.688 -0.344 -0.281
21 C17 C C17 N N N 0 -1.444 3.596 -0.611
22 C18 C C18 N N N 0 0.924 -0.248 1.249
23 C19 C C19 N N N 0 -4.279 0.188 -0.177
24 C20 C C20 N N N 0 6.755 -0.68 0.221
25 C21 C C21 N N N 0 -5.623 -0.509 -0.401
26 N5 N N5 N N N 0 -1.689 0.378 1.138
27 N6 N N6 N N N 0 3.009 -0.788 0.125
28 N8 N N8 N N N 0 -1.429 2.515 2.122
29 O11 O O11 N N N 0 -1.765 1.246 -2.293
30 O15 O O15 N N N 0 4.655 -1.415 -1.224
31 H1 H H1 N N N 0 -0.726 -1.943 0.009
32 H2 H H2 N N N 0 -0.68 -1.294 -1.648
33 H3 H H3 N N N 0 5.229 0.646 0.967
34 H4 H H4 N N N 0 5.255 -0.956 1.743
35 H5 H H5 N N N 0 1.667 -2.274 -0.559
36 H6 H H6 N N N 0 2.116 -1.042 -1.777
37 H7 H H7 N N N 0 -3.21 -1.12 -1.513
38 H8 H H8 N N N 0 -3.218 -1.651 0.185
39 H9 H H9 N N N 0 -8.134 -0.604 -1.457
40 H10 H H10 N N N 0 -8.91 0.525 -0.32
41 H11 H H11 N N N 0 8.906 1.358 -1.276
42 H12 H H12 N N N 0 8.964 -0.362 -1.754
43 H18 H H18 N N N 0 -7.161 -2.748 -0.622
44 H13 H H13 N N N 0 9.724 -0.915 0.329
45 H14 H H14 N N N 0 9.668 0.805 0.806
46 H15 H H15 N N N 0 -8.23 -0.921 1.577
47 H16 H H16 N N N 0 -9.22 -1.826 0.407
48 H17 H H17 N N N 0 -7.244 -3.148 1.111
49 H19 H H19 N N N 0 -5.752 -1.234 1.623
50 H20 H H20 N N N 0 -4.976 -2.362 0.485
51 H21 H H21 N N N 0 -6.642 1.31 -0.945
52 H22 H H22 N N N 0 -6.725 0.91 0.788
53 H23 H H23 N N N 0 6.629 1.268 -0.758
54 H24 H H24 N N N 0 6.646 -0.121 -1.889
55 H25 H H25 N N N 0 8.04 -1.136 1.929
56 H26 H H26 N N N 0 7.567 0.587 1.807
57 H27 H H27 N N N 0 2.794 0.835 1.455
58 H28 H H28 N N N 0 2.79 -0.777 2.223
59 H29 H H29 N N N 0 0.73 0.641 -0.746
60 H30 H H30 N N N 0 -1.338 4.214 0.281
61 H31 H H31 N N N 0 -0.566 3.719 -1.244
62 H32 H H32 N N N 0 -2.334 3.902 -1.161
63 H33 H H33 N N N 0 0.528 -1.128 1.756
64 H34 H H34 N N N 0 0.479 0.662 1.652
65 H35 H H35 N N N 0 -4.21 0.519 0.86
66 H36 H H36 N N N 0 -4.202 1.051 -0.839
67 H41 H H41 N N N 0 -1.704 -0.169 1.939
68 H37 H H37 N N N 0 6.857 -1.72 -0.09
69 H38 H H38 N N N 0 -5.656 -0.917 -1.411
70 H39 H H39 N N N 0 -1.335 3.474 2.007



3KO : Chemical Bonds

Total Number of Bonds: 73
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C14 C18 C C sing 1.54 N N
2 C14 N6 C N sing 1.47 N N
3 C18 C16 C C sing 1.55 N N
4 C13 C20 C C sing 1.53 N N
5 C13 C7 C C sing 1.51 N N
6 N6 C7 N C sing 1.35 N N
7 N6 C10 N C sing 1.47 N N
8 C16 C9 C C sing 1.53 N N
9 C16 C10 C C sing 1.55 N N
10 C20 C22 C C sing 1.55 N N
11 C20 C23 C C sing 1.55 N N
12 C7 O15 C O doub 1.21 N N
13 C9 C4 C C sing 1.53 N N
14 C22 C29 C C sing 1.54 N N
15 C23 C28 C C sing 1.54 N N
16 C29 C28 C C sing 1.54 N N
17 C12 C4 C C sing 1.53 N N
18 C12 C19 C C sing 1.53 N N
19 C4 N5 C N sing 1.47 N N
20 C4 C3 C C sing 1.51 N N
21 C27 C24 C C sing 1.53 N N
22 C27 C30 C C sing 1.53 N N
23 C24 C21 C C sing 1.53 N N
24 O11 C3 O C doub 1.21 N N
25 N5 C2 N C sing 1.37 N N
26 C3 N1 C N sing 1.35 N N
27 C21 C19 C C sing 1.53 N N
28 C21 C25 C C sing 1.53 N N
29 C30 C26 C C sing 1.53 N N
30 C2 N1 C N sing 1.37 N N
31 C2 N8 C N doub 1.3 N N
32 N1 C17 N C sing 1.46 N N
33 C26 C25 C C sing 1.53 N N
34 C9 H1 C H sing 1.09 N N
35 C9 H2 C H sing 1.09 N N
36 C13 H3 C H sing 1.09 N N
37 C13 H4 C H sing 1.09 N N
38 C10 H5 C H sing 1.09 N N
39 C10 H6 C H sing 1.09 N N
40 C12 H7 C H sing 1.09 N N
41 C12 H8 C H sing 1.09 N N
42 C27 H9 C H sing 1.09 N N
43 C27 H10 C H sing 1.09 N N
44 C28 H11 C H sing 1.09 N N
45 C28 H12 C H sing 1.09 N N
46 C29 H13 C H sing 1.09 N N
47 C29 H14 C H sing 1.09 N N
48 C30 H15 C H sing 1.09 N N
49 C30 H16 C H sing 1.09 N N
50 C26 H17 C H sing 1.09 N N
51 C26 H18 C H sing 1.09 N N
52 C25 H19 C H sing 1.09 N N
53 C25 H20 C H sing 1.09 N N
54 C24 H21 C H sing 1.09 N N
55 C24 H22 C H sing 1.09 N N
56 C23 H23 C H sing 1.09 N N
57 C23 H24 C H sing 1.09 N N
58 C22 H25 C H sing 1.09 N N
59 C22 H26 C H sing 1.09 N N
60 C14 H27 C H sing 1.09 N N
61 C14 H28 C H sing 1.09 N N
62 C16 H29 C H sing 1.09 N N
63 C17 H30 C H sing 1.09 N N
64 C17 H31 C H sing 1.09 N N
65 C17 H32 C H sing 1.09 N N
66 C18 H33 C H sing 1.09 N N
67 C18 H34 C H sing 1.09 N N
68 C19 H35 C H sing 1.09 N N
69 C19 H36 C H sing 1.09 N N
70 C20 H37 C H sing 1.09 N N
71 C21 H38 C H sing 1.09 N N
72 N8 H39 N H sing 0.97 N N
73 N5 H41 N H sing 0.97 N N



3KO : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
3KO 4r8y Open in New Window Bound ligand 2 1