Chemical Components in the PDB

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LP4 : Summary

Code

LP4

One-letter code

X

Molecule name

2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose
OpenEye OEToolkits 1.7.6 [(2R,3S,4R,5R,6R)-2-(hydroxymethyl)-6-oxidanyl-5-[[(3R)-3-oxidanyltetradecanoyl]amino]-3-phosphonooxy-oxan-4-yl] (3R)-3-oxidanyltetradecanoate

Formula

C34 H66 N O12 P

Formal charge

0

Molecular weight

711.861 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OC1C(OC(O)C(NC(=O)CC(O)CCCCCCCCCCC)C1OC(=O)CC(O)CCCCCCCCCCC)CO
SMILES CACTVS 3.370 CCCCCCCCCCC[CH](O)CC(=O)N[CH]1[CH](O)O[CH](CO)[CH](O[P](O)(O)=O)[CH]1OC(=O)C[CH](O)CCCCCCCCCCC
SMILES OpenEye OEToolkits 1.7.6 CCCCCCCCCCCC(CC(=O)NC1C(C(C(OC1O)CO)OP(=O)(O)O)OC(=O)CC(CCCCCCCCCCC)O)O
Canonical SMILES CACTVS 3.370 CCCCCCCCCCC[C@@H](O)CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O[P](O)(O)=O)[C@@H]1OC(=O)C[C@H](O)CCCCCCCCCCC
Canonical SMILES OpenEye OEToolkits 1.7.6 CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)OP(=O)(O)O)OC(=O)C[C@@H](CCCCCCCCCCC)O)O

IUPAC InChI

InChI=1S/C34H66NO12P/c1-3-5-7-9-11-13-15-17-19-21-26(37)23-29(39)35-31-33(32(47-48(42,43)44)28(25-36)45-34(31)41)46-30(40)24-27(38)22-20-18-16-14-12-10-8-6-4-2/h26-28,31-34,36-38,41H,3-25H2,1-2H3,(H,35,39)(H2,42,43,44)/t26-,27-,28-,31-,32-,33-,34-/m1/s1

IUPAC InChI key

AJRPJFBMHCTNGK-XQJZMFRCSA-N
LP4

wwPDB Information

Atom count

114 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-12-26

Last modified at

2013-01-08

Status

Released

Obsoleted

Not Assigned



LP4 : Atoms of Molecule

Total Number of Atoms: 114
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -4.881 3.118 -1.002
2 C16 C C16 R N N 0 0.527 3.584 -0.26
3 C17 C C17 N N N 0 1.963 3.35 -0.736
4 C18 C C18 N N N 0 2.906 4.303 0.0020
5 C19 C C19 N N N 0 4.341 4.069 -0.473
6 C2 C C2 R N N 0 -4.129 2.037 -0.221
7 C20 C C20 N N N 0 5.284 5.022 0.264
8 C21 C C21 N N N 0 6.72 4.788 -0.211
9 C22 C C22 N N N 0 7.662 5.741 0.527
10 C23 C C23 N N N 0 9.098 5.508 0.051
11 C24 C C24 N N N 0 10.041 6.46 0.789
12 C25 C C25 N N N 0 11.476 6.227 0.314
13 C26 C C26 N N N 0 12.419 7.179 1.051
14 C27 C C27 N N N 0 13.855 6.946 0.576
15 C28 C C28 N N N 0 -3.259 -1.025 -0.156
16 C29 C C29 N N N 0 -2.525 -2.096 0.609
17 C3 C C3 R N N 0 -4.882 0.709 -0.35
18 C30 C C30 R N N 0 -1.493 -2.76 -0.305
19 C31 C C31 N N N 0 -0.663 -3.759 0.503
20 C32 C C32 N N N 0 0.449 -4.331 -0.379
21 C33 C C33 N N N 0 1.278 -5.33 0.43
22 C34 C C34 N N N 0 2.39 -5.902 -0.452
23 C35 C C35 N N N 0 3.22 -6.901 0.356
24 C36 C C36 N N N 0 4.331 -7.473 -0.526
25 C37 C C37 N N N 0 5.161 -8.472 0.282
26 C38 C C38 N N N 0 6.273 -9.044 -0.6
27 C39 C C39 N N N 0 7.102 -10.043 0.209
28 C4 C C4 S N N 0 -6.317 0.897 0.153
29 C40 C C40 N N N 0 8.214 -10.615 -0.674
30 C41 C C41 N N N 0 9.044 -11.615 0.135
31 C5 C C5 R N N 0 -6.984 2.022 -0.642
32 C6 C C6 N N N 0 -8.398 2.257 -0.106
33 C7 C C7 N N N 0 -1.788 2.7 -0.343
34 C8 C C8 N N N 0 -0.398 2.549 -0.904
35 H1 H H1 N N N 0 -4.906 2.853 -2.059
36 H16 H H16 N N N 0 0.484 3.485 0.824
37 H17 H H17 N N N 0 2.251 2.32 -0.528
38 H17A H H17A N N N 0 2.025 3.535 -1.808
39 H18 H H18 N N N 0 2.617 5.333 -0.206
40 H18A H H18A N N N 0 2.844 4.117 1.074
41 H19 H H19 N N N 0 4.63 3.039 -0.265
42 H19A H H19A N N N 0 4.404 4.254 -1.546
43 H2 H H2 N N N 0 -4.069 2.321 0.829
44 H20 H H20 N N N 0 4.996 6.052 0.056
45 H20A H H20A N N N 0 5.222 4.837 1.337
46 H21 H H21 N N N 0 7.008 3.758 -0.0030
47 H21A H H21A N N N 0 6.782 4.974 -1.283
48 H22 H H22 N N N 0 7.374 6.771 0.319
49 H22A H H22A N N N 0 7.6 5.556 1.599
50 H23 H H23 N N N 0 9.387 4.477 0.259
51 H23A H H23A N N N 0 9.16 5.693 -1.021
52 H24 H H24 N N N 0 9.752 7.49 0.581
53 H24A H H24A N N N 0 9.979 6.275 1.861
54 H25 H H25 N N N 0 11.765 5.196 0.522
55 H25A H H25A N N N 0 11.538 6.412 -0.759
56 H26 H H26 N N N 0 12.131 8.21 0.843
57 H26A H H26A N N N 0 12.357 6.994 2.124
58 H27 H H27 N N N 0 13.917 7.131 -0.496
59 H27A H H27A N N N 0 14.526 7.624 1.102
60 H27B H H27B N N N 0 14.143 5.915 0.784
61 H29 H H29 N N N 0 -2.018 -1.649 1.464
62 H29A H H29A N N N 0 -3.235 -2.845 0.959
63 H3 H H3 N N N 0 -4.899 0.399 -1.395
64 H30 H H30 N N N 0 -0.836 -1.998 -0.725
65 H31 H H31 N N N 0 -0.221 -3.254 1.362
66 H31A H H31A N N N 0 -1.305 -4.569 0.849
67 H32 H H32 N N N 0 0.0070 -4.836 -1.238
68 H32A H H32A N N N 0 1.091 -3.521 -0.724
69 H33 H H33 N N N 0 1.72 -4.825 1.289
70 H33A H H33A N N N 0 0.636 -6.14 0.775
71 H34 H H34 N N N 0 1.948 -6.407 -1.311
72 H34A H H34A N N N 0 3.032 -5.092 -0.798
73 H35 H H35 N N N 0 3.661 -6.396 1.215
74 H35A H H35A N N N 0 2.577 -7.711 0.702
75 H36 H H36 N N N 0 3.89 -7.978 -1.385
76 H36A H H36A N N N 0 4.974 -6.663 -0.872
77 H37 H H37 N N N 0 5.602 -7.967 1.141
78 H37A H H37A N N N 0 4.519 -9.282 0.628
79 H38 H H38 N N N 0 5.831 -9.55 -1.459
80 H38A H H38A N N N 0 6.915 -8.234 -0.945
81 H39 H H39 N N N 0 7.544 -9.538 1.068
82 H39A H H39A N N N 0 6.46 -10.854 0.554
83 H4 H H4 N N N 0 -6.301 1.158 1.211
84 H40 H H40 N N N 0 7.772 -11.121 -1.533
85 H40A H H40A N N N 0 8.856 -9.805 -1.019
86 H41 H H41 N N N 0 9.835 -12.022 -0.493
87 H41A H H41A N N N 0 9.485 -11.109 0.994
88 H41B H H41B N N N 0 8.401 -12.425 0.481
89 H5 H H5 N N N 0 -7.036 1.742 -1.695
90 H6 H H6 N N N 0 -8.955 1.32 -0.128
91 H6A H H6A N N N 0 -8.341 2.622 0.919
92 H8 H H8 N N N 0 -0.027 1.547 -0.69
93 H8A H H8A N N N 0 -0.422 2.705 -1.983
94 HN2 H HN2 N N N 0 -2.595 1.209 -1.433
95 HO1 H HO1 N N Y 0 -4.639 5.105 -1.309
96 HO43 H HO43 N N N 0 -2.768 -4.139 -1.063
97 HO44 H HO44 N N N 0 0.123 5.056 -1.591
98 HO46 H HO46 N N N 0 -9.005 -2.897 1.286
99 HO47 H HO47 N N N 0 -5.942 -2.28 1.735
100 HO6 H HO6 N N N 0 -9.965 3.423 -0.639
101 N2 N N2 N N N 0 -2.778 1.89 -0.767
102 O1 O O1 N N Y 0 -4.215 4.372 -0.84
103 O3 O O3 N N N 0 -4.217 -0.306 0.448
104 O4 O O4 N N N 0 -7.049 -0.316 -0.03
105 O42 O O42 N N N 0 -2.985 -0.815 -1.314
106 O43 O O43 N N N 0 -2.165 -3.445 -1.364
107 O44 O O44 N N N 0 0.109 4.897 -0.637
108 O46 O O46 N N N 0 -8.572 -2.364 0.606
109 O47 O O47 N N N 0 -6.568 -1.681 2.165
110 O48 O O48 N N N 0 -8.618 -0.225 1.946
111 O5 O O5 N N N 0 -6.217 3.22 -0.505
112 O6 O O6 N N N 0 -9.062 3.225 -0.921
113 O7 O O7 N N N 0 -2.016 3.552 0.49
114 P45 P P45 N N N 0 -7.721 -1.127 1.189



LP4 : Chemical Bonds

Total Number of Bonds: 114
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 C1 C C sing 1.53 N N
2 C1 O5 C O sing 1.43 N N
3 C1 O1 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 O1 HO1 O H sing 0.97 N N
6 C3 C2 C C sing 1.53 N N
7 N2 C2 N C sing 1.46 N N
8 C2 H2 C H sing 1.09 N N
9 N2 C7 N C sing 1.35 N N
10 N2 HN2 N H sing 0.97 N N
11 O3 C3 O C sing 1.45 N N
12 C3 C4 C C sing 1.53 N N
13 C3 H3 C H sing 1.09 N N
14 C28 O3 C O sing 1.34 N N
15 O4 C4 O C sing 1.43 N N
16 C4 C5 C C sing 1.53 N N
17 C4 H4 C H sing 1.09 N N
18 P45 O4 P O sing 1.61 N N
19 C5 C6 C C sing 1.53 N N
20 C5 O5 C O sing 1.43 N N
21 C5 H5 C H sing 1.09 N N
22 C6 O6 C O sing 1.43 N N
23 C6 H6 C H sing 1.09 N N
24 C6 H6A C H sing 1.09 N N
25 O6 HO6 O H sing 0.97 N N
26 C8 C7 C C sing 1.51 N N
27 C7 O7 C O doub 1.21 N N
28 C8 C16 C C sing 1.53 N N
29 C8 H8 C H sing 1.09 N N
30 C8 H8A C H sing 1.09 N N
31 C17 C16 C C sing 1.53 N N
32 C16 O44 C O sing 1.43 N N
33 C16 H16 C H sing 1.09 N N
34 C17 C18 C C sing 1.53 N N
35 C17 H17 C H sing 1.09 N N
36 C17 H17A C H sing 1.09 N N
37 C19 C18 C C sing 1.53 N N
38 C18 H18 C H sing 1.09 N N
39 C18 H18A C H sing 1.09 N N
40 C19 C20 C C sing 1.53 N N
41 C19 H19 C H sing 1.09 N N
42 C19 H19A C H sing 1.09 N N
43 C20 C21 C C sing 1.53 N N
44 C20 H20 C H sing 1.09 N N
45 C20 H20A C H sing 1.09 N N
46 C22 C21 C C sing 1.53 N N
47 C21 H21 C H sing 1.09 N N
48 C21 H21A C H sing 1.09 N N
49 C23 C22 C C sing 1.53 N N
50 C22 H22 C H sing 1.09 N N
51 C22 H22A C H sing 1.09 N N
52 C24 C23 C C sing 1.53 N N
53 C23 H23 C H sing 1.09 N N
54 C23 H23A C H sing 1.09 N N
55 C25 C24 C C sing 1.53 N N
56 C24 H24 C H sing 1.09 N N
57 C24 H24A C H sing 1.09 N N
58 C26 C25 C C sing 1.53 N N
59 C25 H25 C H sing 1.09 N N
60 C25 H25A C H sing 1.09 N N
61 C27 C26 C C sing 1.53 N N
62 C26 H26 C H sing 1.09 N N
63 C26 H26A C H sing 1.09 N N
64 C27 H27 C H sing 1.09 N N
65 C27 H27A C H sing 1.09 N N
66 C27 H27B C H sing 1.09 N N
67 C29 C28 C C sing 1.51 N N
68 O42 C28 O C doub 1.21 N N
69 C30 C29 C C sing 1.53 N N
70 C29 H29 C H sing 1.09 N N
71 C29 H29A C H sing 1.09 N N
72 C31 C30 C C sing 1.53 N N
73 O43 C30 O C sing 1.43 N N
74 C30 H30 C H sing 1.09 N N
75 C32 C31 C C sing 1.53 N N
76 C31 H31 C H sing 1.09 N N
77 C31 H31A C H sing 1.09 N N
78 C33 C32 C C sing 1.53 N N
79 C32 H32 C H sing 1.09 N N
80 C32 H32A C H sing 1.09 N N
81 C33 C34 C C sing 1.53 N N
82 C33 H33 C H sing 1.09 N N
83 C33 H33A C H sing 1.09 N N
84 C34 C35 C C sing 1.53 N N
85 C34 H34 C H sing 1.09 N N
86 C34 H34A C H sing 1.09 N N
87 C36 C35 C C sing 1.53 N N
88 C35 H35 C H sing 1.09 N N
89 C35 H35A C H sing 1.09 N N
90 C36 C37 C C sing 1.53 N N
91 C36 H36 C H sing 1.09 N N
92 C36 H36A C H sing 1.09 N N
93 C37 C38 C C sing 1.53 N N
94 C37 H37 C H sing 1.09 N N
95 C37 H37A C H sing 1.09 N N
96 C38 C39 C C sing 1.53 N N
97 C38 H38 C H sing 1.09 N N
98 C38 H38A C H sing 1.09 N N
99 C39 C40 C C sing 1.53 N N
100 C39 H39 C H sing 1.09 N N
101 C39 H39A C H sing 1.09 N N
102 C40 C41 C C sing 1.53 N N
103 C40 H40 C H sing 1.09 N N
104 C40 H40A C H sing 1.09 N N
105 C41 H41 C H sing 1.09 N N
106 C41 H41A C H sing 1.09 N N
107 C41 H41B C H sing 1.09 N N
108 O43 HO43 O H sing 0.97 N N
109 O44 HO44 O H sing 0.97 N N
110 O48 P45 O P doub 1.48 N N
111 O47 P45 O P sing 1.61 N N
112 P45 O46 P O sing 1.61 N N
113 O46 HO46 O H sing 0.97 N N
114 O47 HO47 O H sing 0.97 N N



LP4 : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
LP4 2e59 Open in New Window Bound ligand 1 1
LP4 3mu3 Open in New Window Bound ligand 2 1
LP4 3vq1 Open in New Window Bound ligand 2 1
LP4 3vq2 Open in New Window Bound ligand 2 1
LP4 4g8a Open in New Window Bound ligand 2 1
LP4 4lkv Open in New Window Bound ligand 2 1
LP4 5ijd Open in New Window Bound ligand 2 1