Chemical Components in the PDB

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14S : Summary

Code

14S

One-letter code

X

Molecule name

4-(cyclopentylamino)-2-[(2-methoxybenzyl)amino]-N-[3-(2-oxopyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 4-(cyclopentylamino)-2-[(2-methoxybenzyl)amino]-N-[3-(2-oxopyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide
OpenEye OEToolkits 1.7.6 4-(cyclopentylamino)-2-[(2-methoxyphenyl)methylamino]-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide

Formula

C25 H34 N6 O3

Formal charge

0

Molecular weight

466.576 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C4N(CCCNC(=O)c2cnc(nc2NC1CCCC1)NCc3ccccc3OC)CCC4
SMILES CACTVS 3.370 COc1ccccc1CNc2ncc(C(=O)NCCCN3CCCC3=O)c(NC4CCCC4)n2
SMILES OpenEye OEToolkits 1.7.6 COc1ccccc1CNc2ncc(c(n2)NC3CCCC3)C(=O)NCCCN4CCCC4=O
Canonical SMILES CACTVS 3.370 COc1ccccc1CNc2ncc(C(=O)NCCCN3CCCC3=O)c(NC4CCCC4)n2
Canonical SMILES OpenEye OEToolkits 1.7.6 COc1ccccc1CNc2ncc(c(n2)NC3CCCC3)C(=O)NCCCN4CCCC4=O

IUPAC InChI

InChI=1S/C25H34N6O3/c1-34-21-11-5-2-8-18(21)16-27-25-28-17-20(23(30-25)29-19-9-3-4-10-19)24(33)26-13-7-15-31-14-6-12-22(31)32/h2,5,8,11,17,19H,3-4,6-7,9-10,12-16H2,1H3,(H,26,33)(H2,27,28,29,30)

IUPAC InChI key

ZXZLVQGNVOKCAS-UHFFFAOYSA-N
14S

wwPDB Information

Atom count

68 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-10-09

Last modified at

2013-03-08

Status

Released

Obsoleted

Not Assigned



14S : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O33 O O33 N N N 0 -7.642 1.423 -2.106
2 C28 C C28 N N N 0 -7.944 1.666 -0.956
3 C32 C C32 N N N 0 -8.887 2.766 -0.522
4 C34 C C34 N N N 0 -8.61 2.927 0.991
5 C29 C C29 N N N 0 -8.055 1.534 1.36
6 N24 N N24 N N N 0 -7.494 0.993 0.116
7 C21 C C21 N N N 0 -6.56 -0.134 0.053
8 C19 C C19 N N N 0 -5.124 0.387 0.139
9 C15 C C15 N N N 0 -4.149 -0.79 0.073
10 N10 N N10 N N N 0 -2.774 -0.29 0.156
11 C6 C C6 N N N 0 -1.74 -1.153 0.117
12 O11 O O11 N N N 0 -1.948 -2.347 0.013
13 C2 C C2 N Y N 0 -0.359 -0.651 0.2
14 C1 C C1 N Y N 0 0.734 -1.543 0.273
15 N4 N N4 N N N 0 0.529 -2.906 0.269
16 C8 C C8 N N N 0 1.659 -3.817 0.464
17 C14 C C14 N N N 0 2.325 -4.132 -0.891
18 C18 C C18 N N N 0 2.73 -5.623 -0.778
19 C17 C C17 N N N 0 1.544 -6.241 0.002
20 C13 C C13 N N N 0 1.163 -5.159 1.032
21 C5 C C5 N Y N 0 -0.092 0.722 0.202
22 N9 N N9 N Y N 0 1.16 1.132 0.278
23 C7 C C7 N Y N 0 2.163 0.266 0.351
24 N3 N N3 N Y N 0 1.962 -1.044 0.346
25 N12 N N12 N N N 0 3.455 0.743 0.427
26 C16 C C16 N N N 0 3.703 2.187 0.427
27 C20 C C20 N Y N 0 5.186 2.441 0.518
28 C23 C C23 N Y N 0 5.756 2.776 1.731
29 C27 C C27 N Y N 0 7.117 3.01 1.815
30 C30 C C30 N Y N 0 7.909 2.909 0.687
31 C25 C C25 N Y N 0 7.343 2.576 -0.529
32 C22 C C22 N Y N 0 5.98 2.335 -0.615
33 O26 O O26 N N N 0 5.422 2.001 -1.808
34 C31 C C31 N N N 0 6.299 1.909 -2.932
35 H1 H H1 N N N 0 -8.662 3.692 -1.051
36 H2 H H2 N N N 0 -9.922 2.47 -0.691
37 H3 H H3 N N N 0 -7.867 3.704 1.171
38 H4 H H4 N N N 0 -9.531 3.138 1.536
39 H5 H H5 N N N 0 -7.279 1.626 2.119
40 H6 H H6 N N N 0 -8.859 0.891 1.719
41 H7 H H7 N N N 0 -6.751 -0.812 0.885
42 H8 H H8 N N N 0 -6.697 -0.667 -0.888
43 H9 H H9 N N N 0 -4.933 1.065 -0.693
44 H10 H H10 N N N 0 -4.988 0.92 1.08
45 H11 H H11 N N N 0 -4.34 -1.467 0.905
46 H12 H H12 N N N 0 -4.286 -1.322 -0.868
47 H13 H H13 N N N 0 -2.609 0.662 0.238
48 H14 H H14 N N N 0 -0.364 -3.262 0.136
49 H15 H H15 N N N 0 2.386 -3.37 1.143
50 H16 H H16 N N N 0 1.615 -3.991 -1.707
51 H17 H H17 N N N 0 3.206 -3.507 -1.038
52 H18 H H18 N N N 0 2.821 -6.074 -1.766
53 H19 H H19 N N N 0 3.661 -5.728 -0.22
54 H20 H H20 N N N 0 0.709 -6.441 -0.669
55 H21 H H21 N N N 0 1.855 -7.157 0.505
56 H22 H H22 N N N 0 1.649 -5.363 1.986
57 H23 H H23 N N N 0 0.081 -5.131 1.162
58 H24 H H24 N N N 0 -0.9 1.436 0.143
59 H25 H H25 N N N 0 4.199 0.123 0.481
60 H26 H H26 N N N 0 3.316 2.622 -0.494
61 H27 H H27 N N N 0 3.203 2.642 1.282
62 H28 H H28 N N N 0 5.14 2.855 2.614
63 H29 H H29 N N N 0 7.561 3.271 2.764
64 H30 H H30 N N N 0 8.971 3.092 0.755
65 H31 H H31 N N N 0 7.962 2.498 -1.41
66 H32 H H32 N N N 0 6.783 2.872 -3.094
67 H33 H H33 N N N 0 7.057 1.15 -2.74
68 H34 H H34 N N N 0 5.727 1.636 -3.818



14S : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C16 N12 C N sing 1.47 N N
2 C16 C20 C C sing 1.51 N N
3 N12 C7 N C sing 1.38 N N
4 C20 C23 C C doub 1.38 N Y
5 C20 C22 C C sing 1.39 N Y
6 C7 N9 C N doub 1.33 N Y
7 C7 N3 C N sing 1.33 N Y
8 N9 C5 N C sing 1.32 N Y
9 O26 C22 O C sing 1.36 N N
10 O26 C31 O C sing 1.43 N N
11 C23 C27 C C sing 1.38 N Y
12 C22 C25 C C doub 1.39 N Y
13 N3 C1 N C doub 1.33 N Y
14 C5 C2 C C doub 1.4 N Y
15 C27 C30 C C doub 1.38 N Y
16 C25 C30 C C sing 1.38 N Y
17 C1 C2 C C sing 1.41 N Y
18 C1 N4 C N sing 1.38 N N
19 C2 C6 C C sing 1.47 N N
20 C8 N4 C N sing 1.46 N N
21 C8 C13 C C sing 1.54 N N
22 C8 C14 C C sing 1.54 N N
23 C6 O11 C O doub 1.22 N N
24 C6 N10 C N sing 1.35 N N
25 C13 C17 C C sing 1.54 N N
26 N10 C15 N C sing 1.47 N N
27 C14 C18 C C sing 1.55 N N
28 C15 C19 C C sing 1.53 N N
29 C17 C18 C C sing 1.55 N N
30 C19 C21 C C sing 1.53 N N
31 C21 N24 C N sing 1.47 N N
32 N24 C28 N C sing 1.34 N N
33 N24 C29 N C sing 1.47 N N
34 O33 C28 O C doub 1.21 N N
35 C28 C32 C C sing 1.51 N N
36 C29 C34 C C sing 1.54 N N
37 C32 C34 C C sing 1.55 N N
38 C32 H1 C H sing 1.09 N N
39 C32 H2 C H sing 1.09 N N
40 C34 H3 C H sing 1.09 N N
41 C34 H4 C H sing 1.09 N N
42 C29 H5 C H sing 1.09 N N
43 C29 H6 C H sing 1.09 N N
44 C21 H7 C H sing 1.09 N N
45 C21 H8 C H sing 1.09 N N
46 C19 H9 C H sing 1.09 N N
47 C19 H10 C H sing 1.09 N N
48 C15 H11 C H sing 1.09 N N
49 C15 H12 C H sing 1.09 N N
50 N10 H13 N H sing 0.97 N N
51 N4 H14 N H sing 0.97 N N
52 C8 H15 C H sing 1.09 N N
53 C14 H16 C H sing 1.09 N N
54 C14 H17 C H sing 1.09 N N
55 C18 H18 C H sing 1.09 N N
56 C18 H19 C H sing 1.09 N N
57 C17 H20 C H sing 1.09 N N
58 C17 H21 C H sing 1.09 N N
59 C13 H22 C H sing 1.09 N N
60 C13 H23 C H sing 1.09 N N
61 C5 H24 C H sing 1.08 N N
62 N12 H25 N H sing 0.97 N N
63 C16 H26 C H sing 1.09 N N
64 C16 H27 C H sing 1.09 N N
65 C23 H28 C H sing 1.08 N N
66 C27 H29 C H sing 1.08 N N
67 C30 H30 C H sing 1.08 N N
68 C25 H31 C H sing 1.08 N N
69 C31 H32 C H sing 1.09 N N
70 C31 H33 C H sing 1.09 N N
71 C31 H34 C H sing 1.09 N N



14S : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
14S 4ff8 Open in New Window Bound ligand 1 1