Chemical Components in the PDB

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X3D : Summary

Code

X3D

One-letter code

X

Molecule name

(14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate

Systematic names

ProgramVersionName
ACDLabs 12.01 (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate
OpenEye OEToolkits 2.0.7 [(2~{S})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-undecanoyloxy-propan-2-yl] tetradecanoate

Formula

C30 H60 N O8 P

Formal charge

0

Molecular weight

593.773 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NCCOP(O)(=O)OCC(COC(=O)CCCCCCCCCC)OC(=O)CCCCCCCCCCCCC
SMILES CACTVS 3.385 CCCCCCCCCCCCCC(=O)O[CH](COC(=O)CCCCCCCCCC)CO[P](O)(=O)OCCN
SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCCCCCCC(=O)OC(COC(=O)CCCCCCCCCC)COP(=O)(O)OCCN
Canonical SMILES CACTVS 3.385 CCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC)CO[P](O)(=O)OCCN
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC)COP(=O)(O)OCCN

IUPAC InChI

InChI=1S/C30H60NO8P/c1-3-5-7-9-11-13-14-15-17-19-21-23-30(33)39-28(27-38-40(34,35)37-25-24-31)26-36-29(32)22-20-18-16-12-10-8-6-4-2/h28H,3-27,31H2,1-2H3,(H,34,35)/t28-/m0/s1

IUPAC InChI key

BMOFTHAXXFOIRF-NDEPHWFRSA-N
X3D

wwPDB Information

Atom count

100 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-10-26

Last modified at

2023-03-17

Status

Released

Obsoleted

Not Assigned



X3D : Atoms of Molecule

Total Number of Atoms: 100
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C17 C C1 N N N 0 -0.702 3.246 -1.158
2 C12 C C2 N N N 0 4.143 0.705 -1.25
3 C16 C C3 S N N 0 -0.372 2.189 -2.214
4 C11 C C4 N N N 0 5.068 -0.351 -0.642
5 C28 C C5 N N N 0 -3.63 0.491 -1.939
6 C22 C C6 N N N 0 -4.608 1.9 3.719
7 C21 C C7 N N N 0 -3.767 3.036 3.134
8 C36 C C8 N N N 0 -12.239 -4.128 0.076
9 C35 C C9 N N N 0 -10.965 -3.536 0.684
10 C31 C C10 N N N 0 -6.654 -1.223 -0.332
11 C14 C C11 N N N 0 1.775 1.314 -1.664
12 C13 C C12 N N N 0 2.686 0.274 -1.065
13 C10 C C13 N N N 0 6.524 0.079 -0.827
14 C30 C C14 N N N 0 -5.772 -0.657 -1.448
15 C29 C C15 N N N 0 -4.498 -0.066 -0.84
16 C32 C C16 N N N 0 -7.928 -1.814 -0.94
17 C34 C C17 N N N 0 -10.083 -2.971 -0.432
18 C33 C C18 N N N 0 -8.809 -2.379 0.176
19 C37 C C19 N N N 0 -13.121 -4.693 1.192
20 C38 C C20 N N N 0 -14.394 -5.284 0.585
21 C01 C C21 N N N 0 16.976 -3.479 1.473
22 C02 C C22 N N N 0 16.051 -2.423 0.865
23 C03 C C23 N N N 0 14.594 -2.854 1.05
24 C04 C C24 N N N 0 13.669 -1.798 0.442
25 C05 C C25 N N N 0 12.213 -2.228 0.627
26 C06 C C26 N N N 0 11.288 -1.172 0.019
27 C07 C C27 N N N 0 9.831 -1.603 0.204
28 C08 C C28 N N N 0 8.906 -0.547 -0.404
29 C09 C C29 N N N 0 7.45 -0.977 -0.219
30 C26 C C30 N N N 0 -1.67 1.578 -2.748
31 N23 N N1 N N N 0 -3.721 0.85 4.236
32 O15 O O1 N N N 0 0.444 1.147 -1.618
33 O18 O O2 N N N 0 -1.518 2.663 -0.14
34 O20 O O3 N N N 0 -3.045 2.559 1.998
35 O24 O O4 N N N 0 -2.786 4.689 0.67
36 O25 O O5 N N N 0 -0.808 3.939 2.046
37 O27 O O6 N N N 0 -2.454 1.064 -1.639
38 O39 O O7 N N N 0 -3.993 0.422 -3.089
39 O40 O O8 N N N 0 2.243 2.299 -2.185
40 P19 P P1 N N N 0 -2.055 3.489 1.133
41 H1 H H1 N N N 0 0.221 3.618 -0.715
42 H2 H H2 N N N 0 -1.239 4.071 -1.626
43 H3 H H3 N N N 0 4.305 1.66 -0.751
44 H4 H H4 N N N 0 4.359 0.808 -2.313
45 H5 H H5 N N N 0 0.175 2.654 -3.035
46 H6 H H6 N N N 0 4.852 -0.455 0.421
47 H7 H H7 N N N 0 4.905 -1.307 -1.14
48 H8 H H8 N N N 0 -5.227 2.285 4.53
49 H9 H H9 N N N 0 -5.248 1.484 2.94
50 H10 H H10 N N N 0 -4.421 3.854 2.832
51 H11 H H11 N N N 0 -3.065 3.393 3.888
52 H12 H H12 N N N 0 -12.783 -3.348 -0.457
53 H13 H H13 N N N 0 -11.974 -4.925 -0.617
54 H14 H H14 N N N 0 -11.23 -2.738 1.378
55 H15 H H15 N N N 0 -10.421 -4.316 1.217
56 H16 H H16 N N N 0 -6.11 -2.002 0.201
57 H17 H H17 N N N 0 -6.919 -0.425 0.361
58 H18 H H18 N N N 0 2.524 -0.681 -1.563
59 H19 H H19 N N N 0 2.47 0.171 -0.002
60 H20 H H20 N N N 0 6.74 0.183 -1.89
61 H21 H H21 N N N 0 6.687 1.035 -0.328
62 H22 H H22 N N N 0 -5.508 -1.455 -2.141
63 H23 H H23 N N N 0 -6.316 0.122 -1.981
64 H24 H H24 N N N 0 -3.954 -0.846 -0.307
65 H25 H H25 N N N 0 -4.763 0.732 -0.147
66 H26 H H26 N N N 0 -8.472 -1.034 -1.473
67 H27 H H27 N N N 0 -7.663 -2.612 -1.633
68 H28 H H28 N N N 0 -9.819 -3.769 -1.125
69 H29 H H29 N N N 0 -10.627 -2.191 -0.965
70 H30 H H30 N N N 0 -8.266 -3.159 0.709
71 H31 H H31 N N N 0 -9.074 -1.582 0.869
72 H32 H H32 N N N 0 -12.576 -5.473 1.725
73 H33 H H33 N N N 0 -13.385 -3.895 1.885
74 H34 H H34 N N N 0 -14.13 -6.082 -0.109
75 H35 H H35 N N N 0 -15.023 -5.687 1.379
76 H36 H H36 N N N 0 -14.938 -4.505 0.051
77 H37 H H37 N N N 0 16.813 -4.435 0.975
78 H38 H H38 N N N 0 18.014 -3.173 1.341
79 H39 H H39 N N N 0 16.76 -3.583 2.536
80 H40 H H40 N N N 0 16.213 -1.468 1.364
81 H41 H H41 N N N 0 16.267 -2.32 -0.198
82 H42 H H42 N N N 0 14.432 -3.809 0.552
83 H43 H H43 N N N 0 14.378 -2.957 2.113
84 H44 H H44 N N N 0 13.832 -0.842 0.941
85 H45 H H45 N N N 0 13.885 -1.694 -0.621
86 H46 H H46 N N N 0 12.05 -3.184 0.128
87 H47 H H47 N N N 0 11.997 -2.332 1.69
88 H48 H H48 N N N 0 11.45 -0.216 0.518
89 H49 H H49 N N N 0 11.504 -1.069 -1.044
90 H50 H H50 N N N 0 9.669 -2.558 -0.294
91 H51 H H51 N N N 0 9.615 -1.706 1.267
92 H52 H H52 N N N 0 9.068 0.409 0.095
93 H53 H H53 N N N 0 9.122 -0.443 -1.467
94 H54 H H54 N N N 0 7.234 -1.081 0.844
95 H55 H H55 N N N 0 7.287 -1.933 -0.717
96 H56 H H56 N N N 0 -2.242 2.343 -3.273
97 H57 H H57 N N N 0 -1.433 0.765 -3.434
98 H58 H H58 N N N 0 -3.074 1.224 4.913
99 H59 H H59 N N N 0 -4.253 0.087 4.628
100 H61 H H61 N N N 0 -0.282 3.202 2.385



X3D : Chemical Bonds

Total Number of Bonds: 99
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 C02 C C sing 1.53 N N
2 C02 C03 C C sing 1.53 N N
3 C03 C04 C C sing 1.53 N N
4 C38 C37 C C sing 1.53 N N
5 C04 C05 C C sing 1.53 N N
6 C37 C36 C C sing 1.53 N N
7 C05 C06 C C sing 1.53 N N
8 C36 C35 C C sing 1.53 N N
9 C06 C07 C C sing 1.53 N N
10 C07 C08 C C sing 1.53 N N
11 C35 C34 C C sing 1.53 N N
12 C34 C33 C C sing 1.53 N N
13 C08 C09 C C sing 1.53 N N
14 C09 C10 C C sing 1.53 N N
15 C33 C32 C C sing 1.53 N N
16 C11 C10 C C sing 1.53 N N
17 C11 C12 C C sing 1.53 N N
18 C32 C31 C C sing 1.53 N N
19 C13 C12 C C sing 1.53 N N
20 C13 C14 C C sing 1.51 N N
21 C31 C30 C C sing 1.53 N N
22 N23 C22 N C sing 1.47 N N
23 C14 O15 C O sing 1.34 N N
24 C14 O40 C O doub 1.21 N N
25 O15 C16 O C sing 1.45 N N
26 C30 C29 C C sing 1.53 N N
27 C29 C28 C C sing 1.51 N N
28 C26 C16 C C sing 1.53 N N
29 C26 O27 C O sing 1.45 N N
30 C22 C21 C C sing 1.53 N N
31 C16 C17 C C sing 1.53 N N
32 C21 O20 C O sing 1.43 N N
33 C28 O27 C O sing 1.34 N N
34 C28 O39 C O doub 1.21 N N
35 O24 P19 O P doub 1.48 N N
36 P19 O20 P O sing 1.61 N N
37 P19 O18 P O sing 1.61 N N
38 P19 O25 P O sing 1.61 N N
39 C17 O18 C O sing 1.43 N N
40 C17 H1 C H sing 1.09 N N
41 C17 H2 C H sing 1.09 N N
42 C12 H3 C H sing 1.09 N N
43 C12 H4 C H sing 1.09 N N
44 C16 H5 C H sing 1.09 N N
45 C11 H6 C H sing 1.09 N N
46 C11 H7 C H sing 1.09 N N
47 C22 H8 C H sing 1.09 N N
48 C22 H9 C H sing 1.09 N N
49 C21 H10 C H sing 1.09 N N
50 C21 H11 C H sing 1.09 N N
51 C36 H12 C H sing 1.09 N N
52 C36 H13 C H sing 1.09 N N
53 C35 H14 C H sing 1.09 N N
54 C35 H15 C H sing 1.09 N N
55 C31 H16 C H sing 1.09 N N
56 C31 H17 C H sing 1.09 N N
57 C13 H18 C H sing 1.09 N N
58 C13 H19 C H sing 1.09 N N
59 C10 H20 C H sing 1.09 N N
60 C10 H21 C H sing 1.09 N N
61 C30 H22 C H sing 1.09 N N
62 C30 H23 C H sing 1.09 N N
63 C29 H24 C H sing 1.09 N N
64 C29 H25 C H sing 1.09 N N
65 C32 H26 C H sing 1.09 N N
66 C32 H27 C H sing 1.09 N N
67 C34 H28 C H sing 1.09 N N
68 C34 H29 C H sing 1.09 N N
69 C33 H30 C H sing 1.09 N N
70 C33 H31 C H sing 1.09 N N
71 C37 H32 C H sing 1.09 N N
72 C37 H33 C H sing 1.09 N N
73 C38 H34 C H sing 1.09 N N
74 C38 H35 C H sing 1.09 N N
75 C38 H36 C H sing 1.09 N N
76 C01 H37 C H sing 1.09 N N
77 C01 H38 C H sing 1.09 N N
78 C01 H39 C H sing 1.09 N N
79 C02 H40 C H sing 1.09 N N
80 C02 H41 C H sing 1.09 N N
81 C03 H42 C H sing 1.09 N N
82 C03 H43 C H sing 1.09 N N
83 C04 H44 C H sing 1.09 N N
84 C04 H45 C H sing 1.09 N N
85 C05 H46 C H sing 1.09 N N
86 C05 H47 C H sing 1.09 N N
87 C06 H48 C H sing 1.09 N N
88 C06 H49 C H sing 1.09 N N
89 C07 H50 C H sing 1.09 N N
90 C07 H51 C H sing 1.09 N N
91 C08 H52 C H sing 1.09 N N
92 C08 H53 C H sing 1.09 N N
93 C09 H54 C H sing 1.09 N N
94 C09 H55 C H sing 1.09 N N
95 C26 H56 C H sing 1.09 N N
96 C26 H57 C H sing 1.09 N N
97 N23 H58 N H sing 1.01 N N
98 N23 H59 N H sing 1.01 N N
99 O25 H61 O H sing 0.97 N N



X3D : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
X3D 8exh Open in New Window Bound ligand 40 1