Chemical Components in the PDB

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V9T : Summary

Code

V9T

One-letter code

X

Molecule name

4-[[(3S)-3-cyclopropyl-2-azaspiro[3.3]heptan-2-yl]methyl]-N-[[(3R)-1-[6-(methylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-2-oxidanyl-benzamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 4-[[(3~{S})-3-cyclopropyl-2-azaspiro[3.3]heptan-2-yl]methyl]-~{N}-[[(3~{R})-1-[6-(methylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-2-oxidanyl-benzamide

Formula

C28 H38 N6 O3

Formal charge

0

Molecular weight

506.64 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CNc1cc(ncn1)N2CCC[C](O)(CNC(=O)c3ccc(CN4CC5(CCC5)[CH]4C6CC6)cc3O)C2
SMILES OpenEye OEToolkits 2.0.7 CNc1cc(ncn1)N2CCCC(C2)(CNC(=O)c3ccc(cc3O)CN4CC5(C4C6CC6)CCC5)O
Canonical SMILES CACTVS 3.385 CNc1cc(ncn1)N2CCC[C@@](O)(CNC(=O)c3ccc(CN4CC5(CCC5)[C@@H]4C6CC6)cc3O)C2
Canonical SMILES OpenEye OEToolkits 2.0.7 CNc1cc(ncn1)N2CCC[C@](C2)(CNC(=O)c3ccc(cc3O)CN4CC5([C@@H]4C6CC6)CCC5)O

IUPAC InChI

InChI=1S/C28H38N6O3/c1-29-23-13-24(32-18-31-23)33-11-3-10-28(37,17-33)15-30-26(36)21-7-4-19(12-22(21)35)14-34-16-27(8-2-9-27)25(34)20-5-6-20/h4,7,12-13,18,20,25,35,37H,2-3,5-6,8-11,14-17H2,1H3,(H,30,36)(H,29,31,32)/t25-,28+/m0/s1

IUPAC InChI key

JWBZACHWPMPYIU-LBNVMWSVSA-N
V9T

wwPDB Information

Atom count

75 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-05-03

Last modified at

2021-10-15

Status

Released

Obsoleted

Not Assigned



V9T : Atoms of Molecule

Total Number of Atoms: 75
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 4.643 -0.664 -0.08
2 C15 C C2 N Y N 0 -1.499 -1.435 0.585
3 C17 C C3 N Y N 0 -3.062 0.306 1.131
4 C21 C C4 S N N 0 -7.421 0.958 0.293
5 C22 C C5 N N N 0 -7.371 2.472 0.076
6 C24 C C6 N N N 0 -6.781 3.328 1.198
7 C26 C C7 N N N 0 -9.441 -0.214 -0.996
8 C28 C C8 N N N 0 -8.104 0.827 -2.282
9 C01 C C9 N N N 0 10.005 2.909 0.039
10 C03 C C10 N Y N 0 9.196 0.604 -0.323
11 C04 C C11 N Y N 0 7.893 1.038 -0.102
12 C05 C C12 N Y N 0 6.866 0.102 -0.174
13 C07 C C13 N N N 0 5.162 1.564 -0.878
14 C08 C C14 N N N 0 3.758 2.059 -0.52
15 C09 C C15 N N N 0 2.77 0.894 -0.626
16 C11 C C16 R N N 0 3.224 -0.236 0.301
17 C12 C C17 N N N 0 2.275 -1.428 0.157
18 C14 C C18 N N N 0 -0.114 -1.876 0.334
19 C16 C C19 N Y N 0 -1.765 -0.1 0.898
20 C18 C C20 N Y N 0 -4.103 -0.604 1.057
21 C19 C C21 N N N 0 -5.516 -0.148 1.314
22 C23 C C22 N N N 0 -8.289 3.34 0.939
23 C25 C C23 N N N 0 -7.972 0.189 -0.902
24 C27 C C24 N N N 0 -9.267 -0.152 -2.525
25 C29 C C25 N N N 0 -6.877 -0.821 -0.581
26 C30 C C26 N Y N 0 -3.854 -1.926 0.743
27 C31 C C27 N Y N 0 -2.556 -2.352 0.505
28 C36 C C28 N Y N 0 8.412 -1.538 -0.652
29 N02 N N1 N N N 0 10.255 1.497 -0.259
30 N06 N N2 N N N 0 5.55 0.484 0.038
31 N13 N N3 N N N 0 0.899 -0.99 0.406
32 N20 N N4 N N N 0 -6.128 0.285 0.051
33 N35 N N5 N Y N 0 7.165 -1.166 -0.449
34 N37 N N6 N Y N 0 9.412 -0.682 -0.594
35 O32 O O1 N N N 0 -2.311 -3.65 0.196
36 O33 O O2 N N N 0 0.114 -3.039 0.062
37 O34 O O3 N N N 0 3.211 0.223 1.654
38 H1 H H1 N N N 0 4.974 -1.459 0.588
39 H2 H H2 N N N 0 4.649 -1.027 -1.108
40 H3 H H3 N N N 0 -3.266 1.338 1.373
41 H4 H H4 N N N 0 -7.885 0.682 1.24
42 H5 H H5 N N N 0 -7.192 2.794 -0.95
43 H6 H H6 N N N 0 -6.428 2.812 2.092
44 H7 H H7 N N N 0 -6.214 4.213 0.911
45 H8 H H8 N N N 0 -9.645 -1.216 -0.618
46 H9 H H9 N N N 0 -10.127 0.537 -0.603
47 H10 H H10 N N N 0 -8.411 1.873 -2.253
48 H13 H H13 N N N 0 9.528 2.996 1.015
49 H11 H H11 N N N 0 -7.242 0.656 -2.928
50 H12 H H12 N N N 0 9.352 3.332 -0.724
51 H14 H H14 N N N 0 10.951 3.451 0.048
52 H15 H H15 N N N 0 7.684 2.075 0.119
53 H16 H H16 N N N 0 5.165 1.191 -1.902
54 H17 H H17 N N N 0 5.87 2.388 -0.79
55 H18 H H18 N N N 0 3.757 2.445 0.499
56 H22 H H22 N N N 0 2.35 -1.832 -0.853
57 H19 H H19 N N N 0 3.464 2.849 -1.211
58 H20 H H20 N N N 0 1.776 1.231 -0.331
59 H21 H H21 N N N 0 2.742 0.532 -1.654
60 H23 H H23 N N N 0 2.547 -2.199 0.878
61 H24 H H24 N N N 0 -0.956 0.613 0.958
62 H25 H H25 N N N 0 -6.093 -0.973 1.734
63 H26 H H26 N N N 0 -5.507 0.684 2.018
64 H27 H H27 N N N 0 -8.714 4.233 0.481
65 H28 H H28 N N N 0 -8.928 2.832 1.662
66 H29 H H29 N N N 0 -8.954 -1.099 -2.966
67 H30 H H30 N N N 0 -10.114 0.297 -3.042
68 H31 H H31 N N N 0 -7.189 -1.593 0.122
69 H33 H H33 N N N 0 -4.672 -2.63 0.687
70 H32 H H32 N N N 0 -6.388 -1.228 -1.466
71 H39 H H39 N N N 0 2.342 0.511 1.964
72 H34 H H34 N N N 0 8.622 -2.574 -0.873
73 H35 H H35 N N N 0 11.161 1.186 -0.41
74 H36 H H36 N N N 0 0.718 -0.062 0.623
75 H38 H H38 N N N 0 -2.336 -3.84 -0.751



V9T : Chemical Bonds

Total Number of Bonds: 80
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C24 C23 C C sing 1.53 N N
2 C24 C22 C C sing 1.53 N N
3 C23 C22 C C sing 1.53 N N
4 C22 C21 C C sing 1.53 N N
5 C19 N20 C N sing 1.47 N N
6 C19 C18 C C sing 1.51 N N
7 C21 N20 C N sing 1.48 N N
8 C21 C25 C C sing 1.52 N N
9 N20 C29 N C sing 1.48 N N
10 C18 C17 C C doub 1.38 N Y
11 C18 C30 C C sing 1.38 N Y
12 C26 C25 C C sing 1.53 N N
13 C26 C27 C C sing 1.54 N N
14 C17 C16 C C sing 1.38 N Y
15 C25 C29 C C sing 1.52 N N
16 C25 C28 C C sing 1.53 N N
17 C30 C31 C C doub 1.39 N Y
18 C16 C15 C C doub 1.4 N Y
19 C01 N02 C N sing 1.46 N N
20 C27 C28 C C sing 1.54 N N
21 C31 C15 C C sing 1.4 N Y
22 C31 O32 C O sing 1.36 N N
23 C15 C14 C C sing 1.48 N N
24 C07 C08 C C sing 1.53 N N
25 C07 N06 C N sing 1.47 N N
26 C08 C09 C C sing 1.53 N N
27 N02 C03 N C sing 1.39 N N
28 O33 C14 O C doub 1.22 N N
29 C14 N13 C N sing 1.35 N N
30 C04 C03 C C doub 1.39 N Y
31 C04 C05 C C sing 1.39 N Y
32 C09 C11 C C sing 1.53 N N
33 N06 C05 N C sing 1.39 N N
34 N06 C10 N C sing 1.47 N N
35 C03 N37 C N sing 1.33 N Y
36 C05 N35 C N doub 1.33 N Y
37 C10 C11 C C sing 1.53 N N
38 N13 C12 N C sing 1.47 N N
39 C11 C12 C C sing 1.53 N N
40 C11 O34 C O sing 1.43 N N
41 N37 C36 N C doub 1.32 N Y
42 N35 C36 N C sing 1.32 N Y
43 C10 H1 C H sing 1.09 N N
44 C10 H2 C H sing 1.09 N N
45 C17 H3 C H sing 1.08 N N
46 C21 H4 C H sing 1.09 N N
47 C22 H5 C H sing 1.09 N N
48 C24 H6 C H sing 1.09 N N
49 C24 H7 C H sing 1.09 N N
50 C26 H8 C H sing 1.09 N N
51 C26 H9 C H sing 1.09 N N
52 C28 H10 C H sing 1.09 N N
53 C28 H11 C H sing 1.09 N N
54 C01 H12 C H sing 1.09 N N
55 C01 H13 C H sing 1.09 N N
56 C01 H14 C H sing 1.09 N N
57 C04 H15 C H sing 1.08 N N
58 C07 H16 C H sing 1.09 N N
59 C07 H17 C H sing 1.09 N N
60 C08 H18 C H sing 1.09 N N
61 C08 H19 C H sing 1.09 N N
62 C09 H20 C H sing 1.09 N N
63 C09 H21 C H sing 1.09 N N
64 C12 H22 C H sing 1.09 N N
65 C12 H23 C H sing 1.09 N N
66 C16 H24 C H sing 1.08 N N
67 C19 H25 C H sing 1.09 N N
68 C19 H26 C H sing 1.09 N N
69 C23 H27 C H sing 1.09 N N
70 C23 H28 C H sing 1.09 N N
71 C27 H29 C H sing 1.09 N N
72 C27 H30 C H sing 1.09 N N
73 C29 H31 C H sing 1.09 N N
74 C29 H32 C H sing 1.09 N N
75 C30 H33 C H sing 1.08 N N
76 C36 H34 C H sing 1.08 N N
77 N02 H35 N H sing 0.97 N N
78 N13 H36 N H sing 0.97 N N
79 O32 H38 O H sing 0.97 N N
80 O34 H39 O H sing 0.97 N N



V9T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
V9T 7oej Open in New Window Bound ligand 1 1