Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

867 : Summary

Code

867

One-letter code

X

Molecule name

methyl 6-[4-[[~{N}-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 methyl 6-[4-[[~{N}-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate

Formula

C30 H38 N10 O7

Formal charge

0

Molecular weight

650.686 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COC(=O)c1cc(O)c2cc(NC(=O)NCCCCNC(=N)NCCC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)ccc2c1
SMILES OpenEye OEToolkits 2.0.7 COC(=O)c1cc2ccc(cc2c(c1)O)NC(=O)NCCCCNC(=N)NCCCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O
Canonical SMILES CACTVS 3.385 COC(=O)c1cc(O)c2cc(NC(=O)NCCCCNC(=N)NCCC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)ccc2c1
Canonical SMILES OpenEye OEToolkits 2.0.7 [H]/N=C(\NCCCCNC(=O)Nc1ccc2cc(cc(c2c1)O)C(=O)OC)/NCCC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O

IUPAC InChI

InChI=1S/C30H38N10O7/c1-46-28(44)17-11-16-6-7-18(13-19(16)20(41)12-17)39-30(45)35-9-3-2-8-33-29(32)34-10-4-5-21-23(42)24(43)27(47-21)40-15-38-22-25(31)36-14-37-26(22)40/h6-7,11-15,21,23-24,27,41-43H,2-5,8-10H2,1H3,(H2,31,36,37)(H3,32,33,34)(H2,35,39,45)/t21-,23-,24-,27-/m1/s1

IUPAC InChI key

DMXKZVDCWGJXLG-VBHAUSMQSA-N
867

wwPDB Information

Atom count

85 (47 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-10-04

Last modified at

2022-08-22

Status

Released

Obsoleted

Not Assigned



867 : Atoms of Molecule

Total Number of Atoms: 85
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 13.306 -1.164 -0.376
2 C2 C C2 N Y N 0 13.351 0.218 -0.119
3 C3 C C3 N Y N 0 12.218 0.907 0.19
4 N1 N N1 N N N 0 7.427 0.917 0.937
5 C5 C C4 N Y N 0 10.925 -1.162 -0.004
6 C6 C C5 N Y N 0 12.104 -1.852 -0.32
7 C11 C C6 N N N 0 14.548 -1.886 -0.714
8 C12 C C7 N N N 0 16.9 -1.997 -1.109
9 C13 C C8 N N N 0 6.259 0.539 0.38
10 C16 C C9 N N N 0 1.371 1.105 0.132
11 C17 C C10 N N N 0 -2.214 2.112 0.523
12 C10 C C11 N Y N 0 9.69 -1.832 0.061
13 C14 C C12 N N N 0 3.839 0.716 0.158
14 C15 C C13 N N N 0 2.697 1.534 0.764
15 C18 C C14 N N N 0 -7.13 2.426 0.026
16 C19 C C15 R N N 0 -8.297 1.818 -0.754
17 C20 C C16 S N N 0 -9.61 2.562 -0.424
18 C21 C C17 R N N 0 -10.679 1.447 -0.406
19 C22 C C18 R N N 0 -9.886 0.161 -0.728
20 C23 C C19 N Y N 0 -9.931 -1.416 1.241
21 C24 C C20 N Y N 0 -11.594 -2.712 0.733
22 C25 C C21 N Y N 0 -12.618 -3.67 0.636
23 C26 C C22 N Y N 0 -13.26 -2.728 -1.371
24 C27 C C23 N Y N 0 -11.469 -1.767 -0.299
25 C28 C C24 N N N 0 0.229 1.923 0.738
26 C29 C C25 N N N 0 -4.656 2.366 0.371
27 C30 C C26 N N N 0 -5.823 1.758 -0.409
28 C4 C C27 N Y N 0 10.979 0.232 0.254
29 C7 C C28 N Y N 0 9.799 0.919 0.569
30 C8 C C29 N Y N 0 8.605 0.233 0.623
31 C9 C C30 N Y N 0 8.56 -1.143 0.368
32 N10 N N2 N Y N 0 -12.316 -1.812 -1.322
33 N2 N N3 N N N 0 5.109 1.127 0.763
34 N3 N N4 N N N 0 -1.04 1.512 0.133
35 N4 N N5 N N N 0 -3.405 1.727 -0.045
36 N5 N N6 N N N 0 -2.197 3.046 1.432
37 N6 N N7 N Y N 0 -10.409 -0.968 0.046
38 N7 N N8 N Y N 0 -10.627 -2.44 1.642
39 N8 N N9 N N N 0 -12.79 -4.625 1.622
40 N9 N N10 N Y N 0 -13.417 -3.636 -0.426
41 O1 O O1 N N N 0 12.278 2.242 0.435
42 O2 O O2 N N N 0 15.719 -1.223 -0.77
43 O3 O O3 N N N 0 14.514 -3.079 -0.942
44 O4 O O4 N N N 0 6.244 -0.333 -0.467
45 O5 O O5 N N N 0 -9.908 3.526 -1.436
46 O6 O O6 N N N 0 -11.67 1.688 -1.407
47 O7 O O7 N N N 0 -8.529 0.456 -0.333
48 H1 H H1 N N N 0 14.296 0.74 -0.166
49 H7 H H2 N N N 0 7.45 1.663 1.556
50 H2 H H3 N N N 0 12.076 -2.913 -0.518
51 H9 H H4 N N N 0 17.772 -1.344 -1.119
52 H10 H H5 N N N 0 17.044 -2.783 -0.367
53 H8 H H6 N N N 0 16.77 -2.446 -2.093
54 H17 H H7 N N N 0 1.41 1.277 -0.944
55 H16 H H8 N N N 0 1.203 0.046 0.325
56 H5 H H9 N N N 0 9.64 -2.894 -0.133
57 H13 H H10 N N N 0 3.671 -0.343 0.351
58 H12 H H11 N N N 0 3.878 0.888 -0.918
59 H15 H H12 N N N 0 2.866 2.593 0.571
60 H14 H H13 N N N 0 2.659 1.362 1.84
61 H21 H H14 N N N 0 -7.076 3.496 -0.176
62 H22 H H15 N N N 0 -7.283 2.265 1.093
63 H23 H H16 N N N 0 -8.098 1.857 -1.825
64 H24 H H17 N N N 0 -9.541 3.044 0.552
65 H26 H H18 N N N 0 -11.142 1.377 0.578
66 H28 H H19 N N N 0 -9.932 -0.056 -1.795
67 H29 H H20 N N N 0 -9.094 -0.989 1.774
68 H32 H H21 N N N 0 -13.933 -2.737 -2.217
69 H33 H H22 N N N 0 0.191 1.751 1.814
70 H34 H H23 N N N 0 0.398 2.982 0.545
71 H36 H H24 N N N 0 -4.602 3.436 0.169
72 H35 H H25 N N N 0 -4.809 2.205 1.438
73 H38 H H26 N N N 0 -5.878 0.688 -0.207
74 H37 H H27 N N N 0 -5.67 1.919 -1.476
75 H3 H H28 N N N 0 9.825 1.981 0.768
76 H4 H H29 N N N 0 7.614 -1.663 0.416
77 H11 H H30 N N N 0 5.121 1.822 1.439
78 H18 H H31 N N N 0 -1.053 0.817 -0.543
79 H19 H H32 N N N 0 -3.417 1.031 -0.721
80 H20 H H33 N N N 0 -1.357 3.318 1.833
81 H31 H H34 N N N 0 -12.2 -4.639 2.392
82 H30 H H35 N N N 0 -13.5 -5.281 1.543
83 H6 H H36 N N N 0 12.162 2.792 -0.351
84 H25 H H37 N N N 0 -10.723 4.022 -1.279
85 H27 H H38 N N N 0 -12.158 2.514 -1.287



867 : Chemical Bonds

Total Number of Bonds: 89
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C11 O C doub 1.22 N N
2 O1 C3 O C sing 1.36 N N
3 N8 C25 N C sing 1.38 N N
4 C2 C3 C C doub 1.36 N Y
5 C2 C1 C C sing 1.41 N Y
6 C11 C1 C C sing 1.48 N N
7 C11 O2 C O sing 1.35 N N
8 C3 C4 C C sing 1.41 N Y
9 C1 C6 C C doub 1.39 N Y
10 N7 C24 N C sing 1.35 N Y
11 N7 C23 N C doub 1.3 N Y
12 O2 C12 O C sing 1.45 N N
13 C25 C24 C C doub 1.41 N Y
14 C25 N9 C N sing 1.33 N Y
15 C24 C27 C C sing 1.4 N Y
16 C4 C7 C C doub 1.4 N Y
17 C4 C5 C C sing 1.42 N Y
18 N9 C26 N C doub 1.32 N Y
19 C23 N6 C N sing 1.36 N Y
20 C6 C5 C C sing 1.4 N Y
21 C7 C8 C C sing 1.38 N Y
22 C5 C10 C C doub 1.41 N Y
23 C27 N6 C N sing 1.37 N Y
24 C27 N10 C N doub 1.33 N Y
25 O4 C13 O C doub 1.22 N N
26 C26 N10 C N sing 1.32 N Y
27 N6 C22 N C sing 1.47 N N
28 C29 N4 C N sing 1.47 N N
29 C29 C30 C C sing 1.53 N N
30 C8 N1 C N sing 1.4 N N
31 C8 C9 C C doub 1.4 N Y
32 N4 C17 N C sing 1.37 N N
33 C13 N1 C N sing 1.35 N N
34 C13 N2 C N sing 1.35 N N
35 C10 C9 C C sing 1.36 N Y
36 C30 C18 C C sing 1.53 N N
37 C14 N2 C N sing 1.47 N N
38 C14 C15 C C sing 1.53 N N
39 C22 C21 C C sing 1.54 N N
40 C22 O7 C O sing 1.44 N N
41 C18 C19 C C sing 1.53 N N
42 C21 O6 C O sing 1.43 N N
43 C21 C20 C C sing 1.54 N N
44 O7 C19 O C sing 1.44 N N
45 C15 C16 C C sing 1.53 N N
46 C17 N5 C N doub 1.3 N N
47 C17 N3 C N sing 1.37 N N
48 C19 C20 C C sing 1.54 N N
49 C16 C28 C C sing 1.53 N N
50 C20 O5 C O sing 1.43 N N
51 N3 C28 N C sing 1.46 N N
52 C2 H1 C H sing 1.08 N N
53 N1 H7 N H sing 0.97 N N
54 C6 H2 C H sing 1.08 N N
55 C12 H9 C H sing 1.09 N N
56 C12 H10 C H sing 1.09 N N
57 C12 H8 C H sing 1.09 N N
58 C16 H17 C H sing 1.09 N N
59 C16 H16 C H sing 1.09 N N
60 C10 H5 C H sing 1.08 N N
61 C14 H13 C H sing 1.09 N N
62 C14 H12 C H sing 1.09 N N
63 C15 H15 C H sing 1.09 N N
64 C15 H14 C H sing 1.09 N N
65 C18 H21 C H sing 1.09 N N
66 C18 H22 C H sing 1.09 N N
67 C19 H23 C H sing 1.09 N N
68 C20 H24 C H sing 1.09 N N
69 C21 H26 C H sing 1.09 N N
70 C22 H28 C H sing 1.09 N N
71 C23 H29 C H sing 1.08 N N
72 C26 H32 C H sing 1.08 N N
73 C28 H33 C H sing 1.09 N N
74 C28 H34 C H sing 1.09 N N
75 C29 H36 C H sing 1.09 N N
76 C29 H35 C H sing 1.09 N N
77 C30 H38 C H sing 1.09 N N
78 C30 H37 C H sing 1.09 N N
79 C7 H3 C H sing 1.08 N N
80 C9 H4 C H sing 1.08 N N
81 N2 H11 N H sing 0.97 N N
82 N3 H18 N H sing 0.97 N N
83 N4 H19 N H sing 0.97 N N
84 N5 H20 N H sing 0.97 N N
85 N8 H31 N H sing 0.97 N N
86 N8 H30 N H sing 0.97 N N
87 O1 H6 O H sing 0.97 N N
88 O5 H25 O H sing 0.97 N N
89 O6 H27 O H sing 0.97 N N



867 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
867 7puq Open in New Window Bound ligand 4 1