Chemical Components in the PDB

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P50 : Summary

Code

P50

One-letter code

X

Molecule name

(19S,22S,25R)-25-amino-22-hydroxy-16,22,26-trioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate

Systematic names

ProgramVersionName
ACDLabs 12.01 (19S,22S,25R)-25-amino-22-hydroxy-16,22,26-trioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate
OpenEye OEToolkits 2.0.6 [(2~{S})-1-[[(2~{R})-2-azanyl-3-oxidanylidene-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate

Formula

C40 H76 N O9 P

Formal charge

0

Molecular weight

746.007 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(CCCCCCC[C@H]=[C@H]CCCCCCCC)OC(COC(=O)CCCCCCCCCCCCCCC)COP(O)(=O)OCC(N)C=O
SMILES CACTVS 3.385 CCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](N)C=O)OC(=O)CCCCCCCC=CCCCCCCCC
SMILES OpenEye OEToolkits 2.0.6 CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC(C=O)N)OC(=O)CCCCCCCC=CCCCCCCCC
Canonical SMILES CACTVS 3.385 CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P](O)(=O)OC[C@@H](N)C=O)OC(=O)CCCCCCC\C=C/CCCCCCCC
Canonical SMILES OpenEye OEToolkits 2.0.6 CCCCCCCCCCCCCCCC(=O)OC[C@@H](COP(=O)(O)OC[C@H](C=O)N)OC(=O)CCCCCCC/C=C\CCCCCCCC

IUPAC InChI

InChI=1S/C40H76NO9P/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-40(44)50-38(36-49-51(45,46)48-34-37(41)33-42)35-47-39(43)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h17-18,33,37-38H,3-16,19-32,34-36,41H2,1-2H3,(H,45,46)/b18-17-/t37-,38-/m0/s1

IUPAC InChI key

YXDSQFSRKMJOST-GSXCXXIQSA-N
P50

wwPDB Information

Atom count

127 (51 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-10-18

Last modified at

2017-10-27

Status

Released

Obsoleted

Not Assigned



P50 : Atoms of Molecule

Total Number of Atoms: 127
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O47 O O1 N N N 0 3.166 -4.603 1.478
2 C38 C C1 N N N 0 2.689 -3.493 1.493
3 C39 C C2 N N N 0 3.587 -2.289 1.609
4 C40 C C3 N N N 0 5.045 -2.745 1.69
5 C41 C C4 N N N 0 5.957 -1.522 1.808
6 C42 C C5 N N N 0 7.415 -1.979 1.888
7 C43 C C6 N N N 0 8.327 -0.756 2.006
8 C44 C C7 N N N 0 9.785 -1.212 2.087
9 C45 C C8 N N N 0 10.696 0.011 2.204
10 C46 C C9 N N N 0 12.132 -0.439 2.284
11 C48 C C10 N N N 0 13.023 0.065 1.467
12 C49 C C11 N N N 0 12.653 1.214 0.564
13 C50 C C12 N N N 0 13.648 2.359 0.76
14 C51 C C13 N N N 0 13.272 3.524 -0.157
15 C52 C C14 N N N 0 14.267 4.669 0.04
16 C53 C C15 N N N 0 13.891 5.835 -0.877
17 C54 C C16 N N N 0 14.887 6.98 -0.68
18 C55 C C17 N N N 0 14.51 8.146 -1.597
19 C56 C C18 N N N 0 15.506 9.291 -1.401
20 O37 O O2 N N N 0 1.36 -3.333 1.403
21 C2 C C19 S N N 0 0.557 -4.537 1.288
22 C3 C C20 N N N 0 0.381 -4.894 -0.19
23 O16 O O3 N N N 0 -0.376 -3.872 -0.84
24 P12 P P1 N N N 0 -0.753 -3.92 -2.404
25 O13 O O4 N N N 0 -1.733 -5.166 -2.682
26 O15 O O5 N N N 0 0.483 -4.076 -3.204
27 OG O O6 N N N 0 -1.492 -2.552 -2.821
28 CB C C21 N N N 0 -1.86 -2.244 -4.167
29 CA C C22 R N N 0 -2.54 -0.874 -4.21
30 N N N1 N N N 0 -1.576 0.164 -3.823
31 C C C23 N N N 0 -3.037 -0.604 -5.607
32 O O O7 N N N 0 -2.629 0.355 -6.217
33 C1 C C24 N N N 0 -0.815 -4.298 1.921
34 O19 O O8 N N N 0 -1.529 -3.287 1.163
35 C17 C C25 N N N 0 -2.758 -2.958 1.59
36 O18 O O9 N N N 0 -3.222 -3.498 2.567
37 C20 C C26 N N N 0 -3.559 -1.917 0.853
38 C21 C C27 N N N 0 -4.913 -1.732 1.542
39 C22 C C28 N N N 0 -5.727 -0.675 0.793
40 C23 C C29 N N N 0 -7.08 -0.491 1.482
41 C24 C C30 N N N 0 -7.894 0.567 0.734
42 C25 C C31 N N N 0 -9.247 0.751 1.423
43 C26 C C32 N N N 0 -10.061 1.809 0.674
44 C27 C C33 N N N 0 -11.415 1.993 1.363
45 C28 C C34 N N N 0 -12.228 3.051 0.614
46 C29 C C35 N N N 0 -13.582 3.235 1.303
47 C30 C C36 N N N 0 -14.395 4.293 0.554
48 C31 C C37 N N N 0 -15.749 4.477 1.243
49 C32 C C38 N N N 0 -16.562 5.535 0.495
50 C33 C C39 N N N 0 -17.916 5.719 1.184
51 C34 C C40 N N N 0 -18.729 6.777 0.435
52 H1 H H1 N N N 0 3.454 -1.651 0.735
53 H7 H H7 N N N 0 7.548 -2.616 2.763
54 H2 H H2 N N N 0 3.331 -1.729 2.509
55 H3 H H3 N N N 0 5.178 -3.383 2.564
56 H4 H H4 N N N 0 5.301 -3.304 0.79
57 H5 H H5 N N N 0 5.824 -0.885 0.933
58 H6 H H6 N N N 0 5.701 -0.963 2.707
59 H8 H H8 N N N 0 7.671 -2.538 0.989
60 H9 H H9 N N N 0 8.194 -0.118 1.132
61 H10 H H10 N N N 0 8.071 -0.197 2.906
62 H11 H H11 N N N 0 9.918 -1.85 2.961
63 H12 H H12 N N N 0 10.041 -1.771 1.187
64 H13 H H13 N N N 0 10.563 0.648 1.33
65 H14 H H14 N N N 0 10.44 0.57 3.104
66 H15 H H15 N N N 0 12.427 -1.177 3.015
67 H16 H H16 N N N 0 14.023 -0.342 1.44
68 H17 H H17 N N N 0 12.68 0.883 -0.475
69 H18 H H18 N N N 0 11.648 1.559 0.809
70 H19 H H19 N N N 0 13.621 2.69 1.798
71 H20 H H20 N N N 0 14.652 2.013 0.515
72 H21 H H21 N N N 0 13.299 3.194 -1.195
73 H22 H H22 N N N 0 12.268 3.87 0.089
74 H23 H H23 N N N 0 14.24 5.0 1.078
75 H24 H H24 N N N 0 15.272 4.324 -0.206
76 H25 H H25 N N N 0 13.918 5.504 -1.915
77 H26 H H26 N N N 0 12.887 6.181 -0.632
78 H27 H H27 N N N 0 14.86 7.311 0.358
79 H28 H H28 N N N 0 15.891 6.635 -0.926
80 H29 H H29 N N N 0 14.537 7.815 -2.635
81 H30 H H30 N N N 0 13.506 8.492 -1.352
82 H31 H H31 N N N 0 15.479 9.622 -0.363
83 H32 H H32 N N N 0 16.51 8.946 -1.646
84 H33 H H33 N N N 0 15.238 10.122 -2.054
85 H34 H H34 N N N 0 1.057 -5.358 1.803
86 H35 H H35 N N N 0 1.36 -4.977 -0.662
87 H36 H H36 N N N 0 -0.145 -5.845 -0.274
88 H37 H H37 N N N 0 -2.565 -5.13 -2.19
89 H38 H H38 N N N 0 -0.967 -2.226 -4.792
90 H39 H H39 N N N 0 -2.548 -3.003 -4.538
91 H40 H H40 N N N 0 -3.382 -0.865 -3.517
92 H45 H H45 N N N 0 -1.385 -5.227 1.915
93 H41 H H41 N N N 0 -0.786 0.175 -4.451
94 H42 H H42 N N N 0 -2.017 1.07 -3.781
95 H44 H H44 N N N 0 -3.757 -1.267 -6.062
96 H46 H H46 N N N 0 -0.686 -3.958 2.949
97 H50 H H50 N N N 0 -4.756 -1.409 2.571
98 H47 H H47 N N N 0 -3.018 -0.971 0.858
99 H48 H H48 N N N 0 -3.717 -2.24 -0.176
100 H49 H H49 N N N 0 -5.455 -2.678 1.537
101 H51 H H51 N N N 0 -5.185 0.271 0.798
102 H52 H H52 N N N 0 -5.884 -0.998 -0.236
103 H53 H H53 N N N 0 -7.622 -1.436 1.477
104 H54 H H54 N N N 0 -6.923 -0.167 2.511
105 H55 H H55 N N N 0 -7.352 1.513 0.739
106 H56 H H56 N N N 0 -8.051 0.244 -0.295
107 H57 H H57 N N N 0 -9.789 -0.194 1.418
108 H58 H H58 N N N 0 -9.09 1.075 2.451
109 H59 H H59 N N N 0 -9.519 2.755 0.679
110 H60 H H60 N N N 0 -10.218 1.486 -0.355
111 H61 H H61 N N N 0 -11.956 1.048 1.358
112 H62 H H62 N N N 0 -11.257 2.317 2.392
113 H63 H H63 N N N 0 -11.686 3.997 0.619
114 H64 H H64 N N N 0 -12.385 2.728 -0.415
115 H65 H H65 N N N 0 -14.123 2.289 1.298
116 H66 H H66 N N N 0 -13.425 3.559 2.332
117 H67 H H67 N N N 0 -13.853 5.239 0.559
118 H68 H H68 N N N 0 -14.552 3.97 -0.475
119 H69 H H69 N N N 0 -16.291 3.531 1.238
120 H70 H H70 N N N 0 -15.592 4.801 2.272
121 H71 H H71 N N N 0 -16.02 6.481 0.5
122 H72 H H72 N N N 0 -16.719 5.211 -0.534
123 H73 H H73 N N N 0 -18.458 4.773 1.179
124 H74 H H74 N N N 0 -17.759 6.043 2.213
125 H75 H H75 N N N 0 -18.188 7.723 0.44
126 H76 H H76 N N N 0 -18.886 6.453 -0.594
127 H77 H H77 N N N 0 -19.694 6.908 0.926



P50 : Chemical Bonds

Total Number of Bonds: 126
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C56 C55 C C sing 1.53 N N
2 C55 C54 C C sing 1.53 N N
3 C54 C53 C C sing 1.53 N N
4 C53 C52 C C sing 1.53 N N
5 C52 C51 C C sing 1.53 N N
6 C51 C50 C C sing 1.53 N N
7 C50 C49 C C sing 1.53 N N
8 N CA N C sing 1.47 N N
9 C49 C48 C C sing 1.51 N N
10 C48 C46 C C doub 1.31 Z N
11 C CA C C sing 1.51 N N
12 C O C O doub 1.21 N N
13 CA CB C C sing 1.53 N N
14 C46 C45 C C sing 1.51 N N
15 O15 P12 O P doub 1.48 N N
16 CB OG C O sing 1.43 N N
17 C45 C44 C C sing 1.53 N N
18 OG P12 O P sing 1.61 N N
19 P12 O16 P O sing 1.61 N N
20 P12 O13 P O sing 1.61 N N
21 O16 C3 O C sing 1.43 N N
22 C44 C43 C C sing 1.53 N N
23 C43 C42 C C sing 1.53 N N
24 C3 C2 C C sing 1.53 N N
25 C39 C38 C C sing 1.51 N N
26 C39 C40 C C sing 1.53 N N
27 O37 C2 O C sing 1.45 N N
28 O37 C38 O C sing 1.34 N N
29 C42 C41 C C sing 1.53 N N
30 C2 C1 C C sing 1.53 N N
31 C38 O47 C O doub 1.21 N N
32 C41 C40 C C sing 1.53 N N
33 C1 O19 C O sing 1.45 N N
34 O19 C17 O C sing 1.34 N N
35 C34 C33 C C sing 1.53 N N
36 C17 O18 C O doub 1.21 N N
37 C17 C20 C C sing 1.51 N N
38 C20 C21 C C sing 1.53 N N
39 C33 C32 C C sing 1.53 N N
40 C32 C31 C C sing 1.53 N N
41 C29 C28 C C sing 1.53 N N
42 C29 C30 C C sing 1.53 N N
43 C27 C28 C C sing 1.53 N N
44 C27 C26 C C sing 1.53 N N
45 C21 C22 C C sing 1.53 N N
46 C30 C31 C C sing 1.53 N N
47 C22 C23 C C sing 1.53 N N
48 C26 C25 C C sing 1.53 N N
49 C24 C23 C C sing 1.53 N N
50 C24 C25 C C sing 1.53 N N
51 C39 H1 C H sing 1.09 N N
52 C39 H2 C H sing 1.09 N N
53 C40 H3 C H sing 1.09 N N
54 C40 H4 C H sing 1.09 N N
55 C41 H5 C H sing 1.09 N N
56 C41 H6 C H sing 1.09 N N
57 C42 H7 C H sing 1.09 N N
58 C42 H8 C H sing 1.09 N N
59 C43 H9 C H sing 1.09 N N
60 C43 H10 C H sing 1.09 N N
61 C44 H11 C H sing 1.09 N N
62 C44 H12 C H sing 1.09 N N
63 C45 H13 C H sing 1.09 N N
64 C45 H14 C H sing 1.09 N N
65 C46 H15 C H sing 1.08 N N
66 C48 H16 C H sing 1.08 N N
67 C49 H17 C H sing 1.09 N N
68 C49 H18 C H sing 1.09 N N
69 C50 H19 C H sing 1.09 N N
70 C50 H20 C H sing 1.09 N N
71 C51 H21 C H sing 1.09 N N
72 C51 H22 C H sing 1.09 N N
73 C52 H23 C H sing 1.09 N N
74 C52 H24 C H sing 1.09 N N
75 C53 H25 C H sing 1.09 N N
76 C53 H26 C H sing 1.09 N N
77 C54 H27 C H sing 1.09 N N
78 C54 H28 C H sing 1.09 N N
79 C55 H29 C H sing 1.09 N N
80 C55 H30 C H sing 1.09 N N
81 C56 H31 C H sing 1.09 N N
82 C56 H32 C H sing 1.09 N N
83 C56 H33 C H sing 1.09 N N
84 C2 H34 C H sing 1.09 N N
85 C3 H35 C H sing 1.09 N N
86 C3 H36 C H sing 1.09 N N
87 O13 H37 O H sing 0.97 N N
88 CB H38 C H sing 1.09 N N
89 CB H39 C H sing 1.09 N N
90 CA H40 C H sing 1.09 N N
91 N H41 N H sing 1.01 N N
92 N H42 N H sing 1.01 N N
93 C H44 C H sing 1.08 N N
94 C1 H45 C H sing 1.09 N N
95 C1 H46 C H sing 1.09 N N
96 C20 H47 C H sing 1.09 N N
97 C20 H48 C H sing 1.09 N N
98 C21 H49 C H sing 1.09 N N
99 C21 H50 C H sing 1.09 N N
100 C22 H51 C H sing 1.09 N N
101 C22 H52 C H sing 1.09 N N
102 C23 H53 C H sing 1.09 N N
103 C23 H54 C H sing 1.09 N N
104 C24 H55 C H sing 1.09 N N
105 C24 H56 C H sing 1.09 N N
106 C25 H57 C H sing 1.09 N N
107 C25 H58 C H sing 1.09 N N
108 C26 H59 C H sing 1.09 N N
109 C26 H60 C H sing 1.09 N N
110 C27 H61 C H sing 1.09 N N
111 C27 H62 C H sing 1.09 N N
112 C28 H63 C H sing 1.09 N N
113 C28 H64 C H sing 1.09 N N
114 C29 H65 C H sing 1.09 N N
115 C29 H66 C H sing 1.09 N N
116 C30 H67 C H sing 1.09 N N
117 C30 H68 C H sing 1.09 N N
118 C31 H69 C H sing 1.09 N N
119 C31 H70 C H sing 1.09 N N
120 C32 H71 C H sing 1.09 N N
121 C32 H72 C H sing 1.09 N N
122 C33 H73 C H sing 1.09 N N
123 C33 H74 C H sing 1.09 N N
124 C34 H75 C H sing 1.09 N N
125 C34 H76 C H sing 1.09 N N
126 C34 H77 C H sing 1.09 N N



P50 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
P50 5wke Open in New Window Bound ligand 1 1