Chemical Components in the PDB

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2Y5 : Summary

Code

2Y5

One-letter code

X

Molecule name

(2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate
OpenEye OEToolkits 1.9.2 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(2R,3S,5R,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate

Formula

C47 H84 O16 P2

Formal charge

0

Molecular weight

967.108 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OCC(OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC)COP(=O)(O)OC1C(O)C(O)C(OP(=O)(O)O)C(O)C1O)CCCCCCCCCCCCCCCCC
SMILES CACTVS 3.385 CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[CH]1[CH](O)[CH](O)[CH](O[P](O)(O)=O)[CH](O)[CH]1O)OC(=O)CCCC=CCC=CCC=CCC=CCCCCC
SMILES OpenEye OEToolkits 1.9.2 CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OC1C(C(C(C(C1O)O)OP(=O)(O)O)O)O)OC(=O)CCCC=CCC=CCC=CCC=CCCCCC
Canonical SMILES CACTVS 3.385 CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@H]1O)OC(=O)CCC\C=C/C/C=C\C\C=C/C\C=C/CCCCC
Canonical SMILES OpenEye OEToolkits 1.9.2 CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC1[C@@H]([C@H](C([C@H]([C@H]1O)O)OP(=O)(O)O)O)O)OC(=O)CCCC=CCC=CCC=CCC=CCCCCC

IUPAC InChI

InChI=1S/C47H84O16P2/c1-3-5-7-9-11-13-15-17-19-20-22-24-26-28-30-32-34-36-41(49)61-39(37-59-40(48)35-33-31-29-27-25-23-21-18-16-14-12-10-8-6-4-2)38-60-65(57,58)63-47-44(52)42(50)46(43(51)45(47)53)62-64(54,55)56/h11,13,17,19,22,24,28,30,39,42-47,50-53H,3-10,12,14-16,18,20-21,23,25-27,29,31-38H2,1-2H3,(H,57,58)(H2,54,55,56)/b13-11-,19-17-,24-22-,30-28-/t39-,42-,43+,44-,45-,46+,47+/m1/s1

IUPAC InChI key

ROKMWIUSHIHOGI-BWTMTLBLSA-N
2Y5

wwPDB Information

Atom count

149 (65 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-05-12

Last modified at

2020-05-26

Status

Released

Obsoleted

Not Assigned



2Y5 : Atoms of Molecule

Total Number of Atoms: 149
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -2.071 4.668 0.331
2 O1 O O1 N N N 0 -0.993 3.831 0.753
3 P1 P P1 N N N 0 0.214 4.358 1.68
4 C2 C C2 R N N 0 -2.102 4.727 -1.198
5 O2 O O2 N N N 0 -0.867 5.262 -1.679
6 C3 C C3 R N N 0 -3.257 5.622 -1.651
7 O3 O O3 N N N 0 -3.285 5.678 -3.079
8 C4 C C4 N N N 0 -4.579 5.049 -1.137
9 O4 O O4 N N N 0 -5.657 5.886 -1.559
10 P4 P P2 N N N 0 -6.864 5.359 -2.486
11 C5 C C5 S N N 0 -4.548 4.99 0.392
12 O5 O O5 N N N 0 -5.783 4.455 0.873
13 C6 C C6 R N N 0 -3.393 4.094 0.845
14 O6 O O6 N N N 0 -3.578 2.778 0.321
15 C7 C C7 N N N 0 2.277 3.246 2.964
16 C8 C C8 R N N 0 2.971 1.89 3.108
17 C9 C C9 N N N 0 1.949 0.837 3.538
18 C10 C C10 N N N 0 4.816 1.9 1.599
19 C11 C C11 N N N 0 -0.148 -0.052 2.834
20 O11 O O7 N N N 0 -0.337 4.958 2.914
21 C12 C C12 N N N 0 5.487 1.54 0.299
22 O12 O O8 N N N 0 1.063 5.465 0.877
23 C13 C C13 N N N 0 6.909 2.104 0.285
24 O13 O O9 N N N 0 1.173 3.123 2.065
25 C14 C C14 N N N 0 7.59 1.738 -1.035
26 C15 C C15 N N N 0 8.991 2.294 -1.048
27 C16 C C16 N N N 0 10.005 1.508 -1.317
28 O16 O O10 N N N 0 3.554 1.508 1.834
29 C17 C C17 N N N 0 9.761 0.093 -1.774
30 O17 O O11 N N N 0 5.414 2.542 2.43
31 C18 C C18 N N N 0 10.496 -0.151 -3.067
32 O18 O O12 N N N 0 0.842 0.824 2.598
33 C19 C C19 N N N 0 11.298 -1.181 -3.18
34 O19 O O13 N N N 0 -0.091 -0.783 3.794
35 C20 C C20 N N N 0 11.361 -2.211 -2.081
36 C21 C C21 N N N 0 11.123 -3.58 -2.662
37 C22 C C22 N N N 0 11.981 -4.545 -2.438
38 C23 C C23 N N N 0 13.108 -4.339 -1.459
39 C24 C C24 N N N 0 13.1 -5.451 -0.442
40 C25 C C25 N N N 0 14.185 -6.153 -0.231
41 C26 C C26 N N N 0 15.483 -5.748 -0.881
42 C27 C C27 N N N 0 16.575 -5.639 0.186
43 C28 C C28 N N N 0 17.893 -5.227 -0.474
44 C29 C C29 N N N 0 18.985 -5.118 0.593
45 C30 C C30 N N N 0 20.302 -4.706 -0.067
46 C31 C C31 N N N 0 -1.329 -0.122 1.901
47 C32 C C32 N N N 0 -2.304 -1.193 2.393
48 C33 C C33 N N N 0 -3.504 -1.265 1.446
49 C34 C C34 N N N 0 -4.479 -2.336 1.938
50 C35 C C35 N N N 0 -5.679 -2.408 0.991
51 C36 C C36 N N N 0 -6.654 -3.479 1.484
52 C37 C C37 N N N 0 -7.853 -3.551 0.537
53 C38 C C38 N N N 0 -8.829 -4.622 1.029
54 C39 C C39 N N N 0 -10.028 -4.694 0.082
55 C40 C C40 N N N 0 -11.003 -5.765 0.574
56 C41 C C41 N N N 0 -12.203 -5.837 -0.373
57 O41 O O14 N N N 0 -7.96 6.527 -2.655
58 C42 C C42 N N N 0 -13.178 -6.908 0.12
59 O42 O O15 N N N 0 -6.29 4.948 -3.932
60 C43 C C43 N N N 0 -14.378 -6.979 -0.827
61 O43 O O16 N N N 0 -7.494 4.18 -1.851
62 C44 C C44 N N N 0 -15.353 -8.05 -0.335
63 C45 C C45 N N N 0 -16.552 -8.122 -1.282
64 C46 C C46 N N N 0 -17.528 -9.193 -0.79
65 C47 C C47 N N N 0 -18.727 -9.265 -1.737
66 H1 H H1 N N N 0 -1.931 5.672 0.73
67 H2 H H2 N N N 0 -2.243 3.723 -1.598
68 H3 H H3 N N N 0 -0.816 5.329 -2.642
69 H4 H H4 N N N 0 -3.116 6.627 -1.251
70 H5 H H5 N N N 0 -2.477 6.032 -3.475
71 H6 H H6 N N N 0 -4.719 4.045 -1.536
72 H7 H H7 N N N 0 -4.407 5.994 0.792
73 H8 H H8 N N N 0 -5.834 4.388 1.836
74 H12 H H12 N N N 0 2.984 3.977 2.573
75 H9 H H9 N N N 0 -3.372 4.052 1.934
76 H10 H H10 N N N 0 -4.398 2.352 0.606
77 H11 H H11 N N N 0 1.916 3.575 3.939
78 H13 H H13 N N N 0 3.757 1.962 3.86
79 H14 H H14 N N N 0 2.423 -0.145 3.554
80 H15 H H15 N N N 0 1.576 1.077 4.534
81 H16 H H16 N N N 0 5.525 0.455 0.198
82 H17 H H17 N N N 0 4.921 1.962 -0.532
83 H18 H H18 N N N 0 1.455 5.141 0.054
84 H19 H H19 N N N 0 6.871 3.188 0.386
85 H20 H H20 N N N 0 7.475 1.681 1.115
86 H21 H H21 N N N 0 7.629 0.654 -1.136
87 H22 H H22 N N N 0 7.024 2.161 -1.865
88 H23 H H23 N N N 0 9.16 3.339 -0.835
89 H25 H H25 N N N 0 11.015 1.875 -1.212
90 H27 H H27 N N N 0 10.121 -0.601 -1.015
91 H28 H H28 N N N 0 8.693 -0.06 -1.929
92 H29 H H29 N N N 0 10.362 0.523 -3.9
93 H31 H H31 N N N 0 11.914 -1.292 -4.06
94 H33 H H33 N N N 0 12.345 -2.181 -1.611
95 H34 H H34 N N N 0 10.596 -1.994 -1.336
96 H35 H H35 N N N 0 10.246 -3.767 -3.264
97 H37 H H37 N N N 0 11.88 -5.488 -2.954
98 H39 H H39 N N N 0 14.058 -4.342 -1.993
99 H40 H H40 N N N 0 12.979 -3.382 -0.953
100 H41 H H41 N N N 0 12.2 -5.669 0.113
101 H43 H H43 N N N 0 14.15 -7.023 0.409
102 H45 H H45 N N N 0 15.77 -6.497 -1.618
103 H46 H H46 N N N 0 15.358 -4.783 -1.372
104 H47 H H47 N N N 0 16.288 -4.889 0.924
105 H48 H H48 N N N 0 16.701 -6.603 0.678
106 H49 H H49 N N N 0 18.18 -5.977 -1.212
107 H50 H H50 N N N 0 17.767 -4.262 -0.965
108 H51 H H51 N N N 0 18.698 -4.368 1.331
109 H52 H H52 N N N 0 19.11 -6.082 1.084
110 H53 H H53 N N N 0 21.08 -4.628 0.693
111 H54 H H54 N N N 0 20.589 -5.456 -0.805
112 H55 H H55 N N N 0 20.177 -3.742 -0.559
113 H56 H H56 N N N 0 -1.832 0.844 1.878
114 H57 H H57 N N N 0 -0.986 -0.377 0.898
115 H58 H H58 N N N 0 -1.801 -2.16 2.416
116 H59 H H59 N N N 0 -2.648 -0.939 3.396
117 H60 H H60 N N N 0 -4.007 -0.299 1.423
118 H61 H H61 N N N 0 -3.16 -1.52 0.443
119 H62 H H62 N N N 0 -3.976 -3.303 1.962
120 H63 H H63 N N N 0 -4.823 -2.082 2.941
121 H64 H H64 N N N 0 -6.182 -1.441 0.968
122 H65 H H65 N N N 0 -5.335 -2.663 -0.011
123 H66 H H66 N N N 0 -6.151 -4.446 1.507
124 H67 H H67 N N N 0 -6.997 -3.224 2.486
125 H68 H H68 N N N 0 -8.356 -2.584 0.514
126 H69 H H69 N N N 0 -7.51 -3.806 -0.466
127 H70 H H70 N N N 0 -8.325 -5.589 1.052
128 H71 H H71 N N N 0 -9.172 -4.367 2.032
129 H72 H H72 N N N 0 -10.531 -3.727 0.059
130 H73 H H73 N N N 0 -9.685 -4.949 -0.921
131 H74 H H74 N N N 0 -10.5 -6.731 0.597
132 H75 H H75 N N N 0 -11.347 -5.51 1.577
133 H76 H H76 N N N 0 -12.706 -4.87 -0.396
134 H77 H H77 N N N 0 -11.859 -6.091 -1.375
135 H78 H H78 N N N 0 -8.717 6.279 -3.202
136 H79 H H79 N N N 0 -12.675 -7.874 0.143
137 H80 H H80 N N N 0 -13.522 -6.653 1.122
138 H81 H H81 N N N 0 -5.863 5.674 -4.407
139 H82 H H82 N N N 0 -14.881 -6.013 -0.85
140 H83 H H83 N N N 0 -14.034 -7.234 -1.83
141 H84 H H84 N N N 0 -14.85 -9.017 -0.312
142 H85 H H85 N N N 0 -15.696 -7.796 0.668
143 H86 H H86 N N N 0 -17.056 -7.156 -1.305
144 H87 H H87 N N N 0 -16.209 -8.377 -2.285
145 H88 H H88 N N N 0 -17.024 -10.16 -0.767
146 H89 H H89 N N N 0 -17.871 -8.939 0.213
147 H90 H H90 N N N 0 -19.422 -10.028 -1.386
148 H91 H H91 N N N 0 -19.23 -8.299 -1.76
149 H92 H H92 N N N 0 -18.384 -9.52 -2.739



2Y5 : Chemical Bonds

Total Number of Bonds: 149
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C16 C15 C C doub 1.31 Z N
2 C16 C17 C C sing 1.51 N N
3 C30 C29 C C sing 1.53 N N
4 C15 C14 C C sing 1.51 N N
5 C18 C17 C C sing 1.51 N N
6 C18 C19 C C doub 1.31 Z N
7 C28 C29 C C sing 1.53 N N
8 C28 C27 C C sing 1.53 N N
9 C19 C20 C C sing 1.51 N N
10 C14 C13 C C sing 1.53 N N
11 C27 C26 C C sing 1.53 N N
12 C13 C12 C C sing 1.53 N N
13 C26 C25 C C sing 1.51 N N
14 C20 C21 C C sing 1.51 N N
15 O17 C10 O C doub 1.21 N N
16 C21 C22 C C doub 1.31 Z N
17 C23 C22 C C sing 1.51 N N
18 C23 C24 C C sing 1.51 N N
19 C12 C10 C C sing 1.51 N N
20 C25 C24 C C doub 1.31 Z N
21 C35 C36 C C sing 1.53 N N
22 C35 C34 C C sing 1.53 N N
23 C36 C37 C C sing 1.53 N N
24 C10 O16 C O sing 1.34 N N
25 C38 C37 C C sing 1.53 N N
26 C38 C39 C C sing 1.53 N N
27 C33 C34 C C sing 1.53 N N
28 C33 C32 C C sing 1.53 N N
29 C42 C43 C C sing 1.53 N N
30 C42 C41 C C sing 1.53 N N
31 C44 C45 C C sing 1.53 N N
32 C44 C43 C C sing 1.53 N N
33 C45 C46 C C sing 1.53 N N
34 C40 C39 C C sing 1.53 N N
35 C40 C41 C C sing 1.53 N N
36 C31 C32 C C sing 1.53 N N
37 C31 C11 C C sing 1.51 N N
38 O16 C8 O C sing 1.45 N N
39 O18 C11 O C sing 1.34 N N
40 O18 C9 O C sing 1.45 N N
41 C8 C9 C C sing 1.53 N N
42 C8 C7 C C sing 1.53 N N
43 C11 O19 C O doub 1.21 N N
44 C47 C46 C C sing 1.53 N N
45 C7 O13 C O sing 1.43 N N
46 O13 P1 O P sing 1.61 N N
47 O5 C5 O C sing 1.43 N N
48 O6 C6 O C sing 1.43 N N
49 O43 P4 O P doub 1.48 N N
50 C6 C5 C C sing 1.53 N N
51 C6 C1 C C sing 1.53 N N
52 C5 C4 C C sing 1.53 N N
53 P1 O1 P O sing 1.61 N N
54 P1 O11 P O doub 1.48 N N
55 P1 O12 P O sing 1.61 N N
56 O1 C1 O C sing 1.43 N N
57 C1 C2 C C sing 1.53 N N
58 P4 O42 P O sing 1.61 N N
59 P4 O4 P O sing 1.61 N N
60 P4 O41 P O sing 1.61 N N
61 C4 O4 C O sing 1.43 N N
62 C4 C3 C C sing 1.53 N N
63 C2 C3 C C sing 1.53 N N
64 C2 O2 C O sing 1.43 N N
65 C3 O3 C O sing 1.43 N N
66 C1 H1 C H sing 1.09 N N
67 C2 H2 C H sing 1.09 N N
68 O2 H3 O H sing 0.97 N N
69 C3 H4 C H sing 1.09 N N
70 O3 H5 O H sing 0.97 N N
71 C4 H6 C H sing 1.09 N N
72 C5 H7 C H sing 1.09 N N
73 O5 H8 O H sing 0.97 N N
74 C6 H9 C H sing 1.09 N N
75 O6 H10 O H sing 0.97 N N
76 C7 H11 C H sing 1.09 N N
77 C7 H12 C H sing 1.09 N N
78 C8 H13 C H sing 1.09 N N
79 C9 H14 C H sing 1.09 N N
80 C9 H15 C H sing 1.09 N N
81 C12 H16 C H sing 1.09 N N
82 C12 H17 C H sing 1.09 N N
83 O12 H18 O H sing 0.97 N N
84 C13 H19 C H sing 1.09 N N
85 C13 H20 C H sing 1.09 N N
86 C14 H21 C H sing 1.09 N N
87 C14 H22 C H sing 1.09 N N
88 C15 H23 C H sing 1.08 N N
89 C16 H25 C H sing 1.08 N N
90 C17 H27 C H sing 1.09 N N
91 C17 H28 C H sing 1.09 N N
92 C18 H29 C H sing 1.08 N N
93 C19 H31 C H sing 1.08 N N
94 C20 H33 C H sing 1.09 N N
95 C20 H34 C H sing 1.09 N N
96 C21 H35 C H sing 1.08 N N
97 C22 H37 C H sing 1.08 N N
98 C23 H39 C H sing 1.09 N N
99 C23 H40 C H sing 1.09 N N
100 C24 H41 C H sing 1.08 N N
101 C25 H43 C H sing 1.08 N N
102 C26 H45 C H sing 1.09 N N
103 C26 H46 C H sing 1.09 N N
104 C27 H47 C H sing 1.09 N N
105 C27 H48 C H sing 1.09 N N
106 C28 H49 C H sing 1.09 N N
107 C28 H50 C H sing 1.09 N N
108 C29 H51 C H sing 1.09 N N
109 C29 H52 C H sing 1.09 N N
110 C30 H53 C H sing 1.09 N N
111 C30 H54 C H sing 1.09 N N
112 C30 H55 C H sing 1.09 N N
113 C31 H56 C H sing 1.09 N N
114 C31 H57 C H sing 1.09 N N
115 C32 H58 C H sing 1.09 N N
116 C32 H59 C H sing 1.09 N N
117 C33 H60 C H sing 1.09 N N
118 C33 H61 C H sing 1.09 N N
119 C34 H62 C H sing 1.09 N N
120 C34 H63 C H sing 1.09 N N
121 C35 H64 C H sing 1.09 N N
122 C35 H65 C H sing 1.09 N N
123 C36 H66 C H sing 1.09 N N
124 C36 H67 C H sing 1.09 N N
125 C37 H68 C H sing 1.09 N N
126 C37 H69 C H sing 1.09 N N
127 C38 H70 C H sing 1.09 N N
128 C38 H71 C H sing 1.09 N N
129 C39 H72 C H sing 1.09 N N
130 C39 H73 C H sing 1.09 N N
131 C40 H74 C H sing 1.09 N N
132 C40 H75 C H sing 1.09 N N
133 C41 H76 C H sing 1.09 N N
134 C41 H77 C H sing 1.09 N N
135 O41 H78 O H sing 0.97 N N
136 C42 H79 C H sing 1.09 N N
137 C42 H80 C H sing 1.09 N N
138 O42 H81 O H sing 0.97 N N
139 C43 H82 C H sing 1.09 N N
140 C43 H83 C H sing 1.09 N N
141 C44 H84 C H sing 1.09 N N
142 C44 H85 C H sing 1.09 N N
143 C45 H86 C H sing 1.09 N N
144 C45 H87 C H sing 1.09 N N
145 C46 H88 C H sing 1.09 N N
146 C46 H89 C H sing 1.09 N N
147 C47 H90 C H sing 1.09 N N
148 C47 H91 C H sing 1.09 N N
149 C47 H92 C H sing 1.09 N N



2Y5 : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
2Y5 4ph7 Open in New Window Bound ligand 4 1
2Y5 6roi Open in New Window Bound ligand 1 1
2Y5 6roj Open in New Window Bound ligand 1 1
2Y5 7oh4 Open in New Window Bound ligand 1 1
2Y5 7oh5 Open in New Window Bound ligand 1 1
2Y5 7oh6 Open in New Window Bound ligand 1 1
2Y5 7oh7 Open in New Window Bound ligand 1 1
2Y5 7pem Open in New Window Bound ligand 1 1
2Y5 8t3o Open in New Window Bound ligand 1 1