Chemical Components in the PDB

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6ES : Summary

Code

6ES

One-letter code

X

Molecule name

(2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate
OpenEye OEToolkits 2.0.4 [(2~{S})-1-[oxidanyl-[(2~{S},3~{S},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-3-pentanoyloxy-propan-2-yl] decanoate

Formula

C24 H45 O13 P

Formal charge

0

Molecular weight

572.58 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CCCCC(OCC(COP(O)(OC1C(C(C(C(C1O)O)O)O)O)=O)OC(=O)CCCCCCCCC)=O
SMILES CACTVS 3.385 CCCCCCCCCC(=O)O[CH](COC(=O)CCCC)CO[P](O)(=O)O[CH]1[CH](O)[CH](O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.4 CCCCCCCCCC(=O)OC(COC(=O)CCCC)COP(=O)(O)OC1C(C(C(C(C1O)O)O)O)O
Canonical SMILES CACTVS 3.385 CCCCCCCCCC(=O)O[C@@H](COC(=O)CCCC)CO[P](O)(=O)O[C@@H]1[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.4 CCCCCCCCCC(=O)O[C@@H](COC(=O)CCCC)COP(=O)(O)OC1[C@@H]([C@H](C([C@@H]([C@@H]1O)O)O)O)O

IUPAC InChI

InChI=1S/C24H45O13P/c1-3-5-7-8-9-10-11-13-18(26)36-16(14-34-17(25)12-6-4-2)15-35-38(32,33)37-24-22(30)20(28)19(27)21(29)23(24)31/h16,19-24,27-31H,3-15H2,1-2H3,(H,32,33)/t16-,19-,20-,21-,22+,23-,24+/m0/s1

IUPAC InChI key

YWVFSDQOBMMIAJ-CLASQLQRSA-N
6ES

wwPDB Information

Atom count

83 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-03-23

Last modified at

2016-05-20

Status

Released

Obsoleted

Not Assigned



6ES : Atoms of Molecule

Total Number of Atoms: 83
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 N N N 0 -4.111 4.807 -3.6
2 C02 C C2 N N N 0 -3.641 3.521 -2.918
3 C03 C C3 N N N 0 -2.696 3.87 -1.766
4 C04 C C4 N N N 0 -2.226 2.584 -1.084
5 C05 C C5 N N N 0 -1.295 2.928 0.051
6 O06 O O1 N N N 0 -1.035 4.084 0.289
7 O07 O O2 N N N 0 -0.756 1.951 0.796
8 C08 C C6 N N N 0 0.131 2.356 1.872
9 C09 C C7 S N N 0 0.644 1.115 2.605
10 C10 C C8 N N N 0 -0.544 0.274 3.078
11 O11 O O3 N N N 0 -1.386 -0.029 1.964
12 P12 P P1 N N N 0 -2.733 -0.9 2.095
13 O13 O O4 N N N 0 -3.801 -0.105 3.001
14 O14 O O5 N N N 0 -2.42 -2.201 2.729
15 C18 C C11 S N N 0 -5.116 -0.581 -1.572
16 O15 O O6 N N N 0 -3.354 -1.153 0.631
17 C16 C C9 N N N 0 -4.495 -1.982 0.402
18 C17 C C10 S N N 0 -5.608 -1.151 -0.24
19 C19 C C12 N N N 0 -4.733 -1.729 -2.507
20 C20 C C13 S N N 0 -3.62 -2.56 -1.866
21 C21 C C14 R N N 0 -4.112 -3.13 -0.534
22 O22 O O7 N N N 0 -3.072 -3.906 0.065
23 O23 O O8 N N N 0 -3.261 -3.632 -2.74
24 O24 O O9 N N N 0 -4.273 -1.197 -3.751
25 O25 O O10 N N N 0 -3.975 0.248 -1.343
26 O26 O O11 N N N 0 -5.967 -0.078 0.634
27 O27 O O12 N N N 0 1.467 0.327 1.704
28 C28 C C15 N N N 0 2.78 0.604 1.679
29 O29 O O13 N N N 0 3.227 1.476 2.385
30 C30 C C16 N N N 0 3.696 -0.173 0.769
31 C31 C C17 N N N 0 5.129 0.337 0.932
32 C32 C C18 N N N 0 6.06 -0.451 0.008
33 C33 C C19 N N N 0 7.493 0.059 0.171
34 C34 C C20 N N N 0 8.423 -0.729 -0.753
35 C35 C C21 N N N 0 9.857 -0.219 -0.59
36 C36 C C22 N N N 0 10.787 -1.008 -1.513
37 C37 C C23 N N N 0 12.22 -0.497 -1.35
38 C38 C C24 N N N 0 13.151 -1.286 -2.274
39 H012 H H1 N N N 0 -3.248 5.348 -3.989
40 H013 H H2 N N N 0 -4.784 4.558 -4.42
41 H011 H H3 N N N 0 -4.635 5.431 -2.877
42 H021 H H4 N N N 0 -4.503 2.98 -2.529
43 H022 H H5 N N N 0 -3.116 2.896 -3.641
44 H031 H H6 N N N 0 -1.833 4.411 -2.155
45 H082 H H10 N N N 0 0.975 2.908 1.458
46 H032 H H7 N N N 0 -3.22 4.495 -1.043
47 H042 H H8 N N N 0 -3.089 2.043 -0.695
48 H041 H H9 N N N 0 -1.702 1.959 -1.807
49 H081 H H11 N N N 0 -0.412 2.992 2.571
50 H091 H H12 N N N 0 1.238 1.421 3.466
51 H102 H H13 N N N 0 -0.179 -0.652 3.521
52 H101 H H14 N N N 0 -1.112 0.834 3.821
53 H1 H H15 N N N 0 -4.053 0.758 2.645
54 H161 H H16 N N N 0 -4.846 -2.388 1.35
55 H171 H H17 N N N 0 -6.479 -1.783 -0.415
56 H181 H H18 N N N 0 -5.909 0.011 -2.029
57 H191 H H19 N N N 0 -5.603 -2.362 -2.682
58 H201 H H20 N N N 0 -2.749 -1.928 -1.691
59 H211 H H21 N N N 0 -4.982 -3.762 -0.709
60 H221 H H22 N N N 0 -2.778 -4.653 -0.474
61 H231 H H23 N N N 0 -2.94 -3.344 -3.605
62 H241 H H24 N N N 0 -4.012 -1.87 -4.395
63 H251 H H25 N N N 0 -3.609 0.644 -2.145
64 H261 H H26 N N N 0 -6.669 0.491 0.29
65 H302 H H27 N N N 0 3.655 -1.231 1.029
66 H301 H H28 N N N 0 3.379 -0.041 -0.266
67 H312 H H29 N N N 0 5.17 1.395 0.672
68 H311 H H30 N N N 0 5.447 0.205 1.966
69 H322 H H31 N N N 0 6.019 -1.509 0.268
70 H321 H H32 N N N 0 5.743 -0.319 -1.026
71 H332 H H33 N N N 0 7.534 1.117 -0.089
72 H351 H H37 N N N 0 9.897 0.839 -0.85
73 H331 H H34 N N N 0 7.81 -0.073 1.206
74 H342 H H35 N N N 0 8.383 -1.787 -0.493
75 H341 H H36 N N N 0 8.106 -0.597 -1.787
76 H352 H H38 N N N 0 10.174 -0.352 0.445
77 H362 H H39 N N N 0 10.746 -2.066 -1.253
78 H361 H H40 N N N 0 10.47 -0.875 -2.548
79 H371 H H41 N N N 0 12.261 0.56 -1.61
80 H372 H H42 N N N 0 12.537 -0.63 -0.316
81 H382 H H43 N N N 0 13.11 -2.344 -2.014
82 H381 H H44 N N N 0 12.833 -1.154 -3.308
83 H383 H H45 N N N 0 14.172 -0.922 -2.158



6ES : Chemical Bonds

Total Number of Bonds: 83
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C38 C37 C C sing 1.53 N N
2 C37 C36 C C sing 1.53 N N
3 C36 C35 C C sing 1.53 N N
4 C35 C34 C C sing 1.53 N N
5 C34 C33 C C sing 1.53 N N
6 C33 C32 C C sing 1.53 N N
7 C32 C31 C C sing 1.53 N N
8 C01 C02 C C sing 1.53 N N
9 C02 C03 C C sing 1.53 N N
10 C31 C30 C C sing 1.53 N N
11 C30 C28 C C sing 1.51 N N
12 C03 C04 C C sing 1.53 N N
13 C04 C05 C C sing 1.51 N N
14 C28 O29 C O doub 1.21 N N
15 C28 O27 C O sing 1.34 N N
16 C05 O07 C O sing 1.34 N N
17 C05 O06 C O doub 1.21 N N
18 O07 C08 O C sing 1.45 N N
19 O27 C09 O C sing 1.45 N N
20 C08 C09 C C sing 1.53 N N
21 C09 C10 C C sing 1.53 N N
22 C10 O11 C O sing 1.43 N N
23 O14 P12 O P doub 1.48 N N
24 O11 P12 O P sing 1.61 N N
25 P12 O13 P O sing 1.61 N N
26 P12 O15 P O sing 1.61 N N
27 O15 C16 O C sing 1.43 N N
28 O26 C17 O C sing 1.43 N N
29 C17 C16 C C sing 1.53 N N
30 C17 C18 C C sing 1.53 N N
31 C16 C21 C C sing 1.53 N N
32 O25 C18 O C sing 1.43 N N
33 O22 C21 O C sing 1.43 N N
34 C18 C19 C C sing 1.53 N N
35 C21 C20 C C sing 1.53 N N
36 O24 C19 O C sing 1.43 N N
37 C19 C20 C C sing 1.53 N N
38 C20 O23 C O sing 1.43 N N
39 C01 H012 C H sing 1.09 N N
40 C01 H013 C H sing 1.09 N N
41 C01 H011 C H sing 1.09 N N
42 C02 H021 C H sing 1.09 N N
43 C02 H022 C H sing 1.09 N N
44 C03 H031 C H sing 1.09 N N
45 C03 H032 C H sing 1.09 N N
46 C04 H042 C H sing 1.09 N N
47 C04 H041 C H sing 1.09 N N
48 C08 H082 C H sing 1.09 N N
49 C08 H081 C H sing 1.09 N N
50 C09 H091 C H sing 1.09 N N
51 C10 H102 C H sing 1.09 N N
52 C10 H101 C H sing 1.09 N N
53 O13 H1 O H sing 0.97 N N
54 C16 H161 C H sing 1.09 N N
55 C17 H171 C H sing 1.09 N N
56 C18 H181 C H sing 1.09 N N
57 C19 H191 C H sing 1.09 N N
58 C20 H201 C H sing 1.09 N N
59 C21 H211 C H sing 1.09 N N
60 O22 H221 O H sing 0.97 N N
61 O23 H231 O H sing 0.97 N N
62 O24 H241 O H sing 0.97 N N
63 O25 H251 O H sing 0.97 N N
64 O26 H261 O H sing 0.97 N N
65 C30 H302 C H sing 1.09 N N
66 C30 H301 C H sing 1.09 N N
67 C31 H312 C H sing 1.09 N N
68 C31 H311 C H sing 1.09 N N
69 C32 H322 C H sing 1.09 N N
70 C32 H321 C H sing 1.09 N N
71 C33 H332 C H sing 1.09 N N
72 C33 H331 C H sing 1.09 N N
73 C34 H342 C H sing 1.09 N N
74 C34 H341 C H sing 1.09 N N
75 C35 H351 C H sing 1.09 N N
76 C35 H352 C H sing 1.09 N N
77 C36 H362 C H sing 1.09 N N
78 C36 H361 C H sing 1.09 N N
79 C37 H371 C H sing 1.09 N N
80 C37 H372 C H sing 1.09 N N
81 C38 H382 C H sing 1.09 N N
82 C38 H381 C H sing 1.09 N N
83 C38 H383 C H sing 1.09 N N



6ES : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6ES 5irz Open in New Window Bound ligand 4 1