Chemical Components in the PDB

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VJ4 : Summary

Code

VJ4

One-letter code

X

Molecule name

2-deoxy-2-{[(1S,3R)-1-hydroxy-3-(pentanoyloxy)undecyl]amino}-4-O-phosphono-alpha-D-glucopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2-deoxy-2-{[(1S,3R)-1-hydroxy-3-(pentanoyloxy)undecyl]amino}-4-O-phosphono-beta-D-glucopyranose
OpenEye OEToolkits 2.0.7 [(1~{S},3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2,4-bis(oxidanyl)-5-phosphonooxy-oxan-3-yl]amino]-1-oxidanyl-undecan-3-yl] pentanoate

Formula

C22 H44 N O11 P

Formal charge

0

Molecular weight

529.559 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N(C(CC(OC(=O)CCCC)CCCCCCCC)O)C1C(OC(C(OP(O)(=O)O)C1O)CO)O
SMILES CACTVS 3.385 CCCCCCCC[CH](C[CH](O)N[CH]1[CH](O)O[CH](CO)[CH](O[P](O)(O)=O)[CH]1O)OC(=O)CCCC
SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCC(CC(NC1C(C(C(OC1O)CO)OP(=O)(O)O)O)O)OC(=O)CCCC
Canonical SMILES CACTVS 3.385 CCCCCCCC[C@H](C[C@H](O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O[P](O)(O)=O)[C@@H]1O)OC(=O)CCCC
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCCCCCC[C@H](C[C@@H](N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)OP(=O)(O)O)O)O)OC(=O)CCCC

IUPAC InChI

InChI=1S/C22H44NO11P/c1-3-5-7-8-9-10-11-15(32-18(26)12-6-4-2)13-17(25)23-19-20(27)21(34-35(29,30)31)16(14-24)33-22(19)28/h15-17,19-25,27-28H,3-14H2,1-2H3,(H2,29,30,31)/t15-,16-,17+,19-,20-,21-,22-/m1/s1

IUPAC InChI key

IXXWGAPLUMTSOK-GHZJMGJXSA-N
VJ4

wwPDB Information

Atom count

79 (35 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

Yes

Standard parent

GCS

Defined at

2020-08-13

Last modified at

2020-08-21

Status

Released

Obsoleted

Not Assigned



VJ4 : Atoms of Molecule

Total Number of Atoms: 79
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N2 N N1 N N N 0 1.391 1.657 0.042
2 P1 P P1 N N N 0 7.344 0.501 0.831
3 O6 O O1 N N N 0 5.605 -1.991 -3.163
4 O10 O O2 N N N 0 -3.542 -0.994 1.461
5 O11 O O3 N N N 0 -2.286 -0.415 -0.262
6 C13 C C1 S N N 0 0.145 1.045 0.522
7 O4 O O4 N N N 0 6.192 0.904 -0.22
8 C14 C C2 N N N 0 -1.045 1.68 -0.2
9 O5 O O5 N N N 0 3.384 -0.955 -1.663
10 C15 C C3 R N N 0 -2.332 0.958 0.207
11 O9 O O6 N N N 0 7.612 -0.951 0.737
12 C16 C C4 N N N 0 -3.534 1.67 -0.416
13 O7 O O7 N N N 0 8.689 1.318 0.491
14 C17 C C5 N N N 0 -4.826 1.025 0.09
15 O8 O O8 N N N 0 6.86 0.863 2.323
16 C18 C C6 N N N 0 -6.029 1.737 -0.533
17 C7 C C7 N N N 0 -7.321 1.093 -0.027
18 C10 C C10 N N N 0 -11.019 1.871 -0.767
19 C8 C C8 N N N 0 -8.524 1.804 -0.65
20 C9 C C9 N N N 0 -9.816 1.16 -0.144
21 C11 C C11 N N N 0 -12.311 1.227 -0.261
22 O2 O O9 N N N 0 0.02 1.261 1.929
23 C12 C C12 N N N 0 -2.945 -1.33 0.466
24 C21 C C13 N N N 0 -2.942 -2.776 0.041
25 C31 C C14 N N N 0 -3.761 -3.602 1.035
26 C41 C C15 N N N 0 -3.758 -5.069 0.603
27 C51 C C16 N N N 0 -4.578 -5.895 1.597
28 O3 O O10 N N N 0 3.974 1.879 1.301
29 C1 C C17 R N N 0 2.321 -0.015 -1.489
30 C2 C C18 R N N 0 2.447 0.648 -0.115
31 C3 C C19 R N N 0 3.819 1.321 -0.005
32 C4 C C20 S N N 0 4.91 0.273 -0.248
33 C5 C C21 R N N 0 4.689 -0.375 -1.617
34 C6 C C22 N N N 0 5.739 -1.465 -1.841
35 HN21 H H1 N N N 0 1.69 2.4 0.656
36 HO6 H H3 N N N 0 6.241 -2.688 -3.375
37 H37 H H4 N N N 0 0.165 -0.025 0.319
38 H38 H H5 N N N 0 -1.117 2.732 0.073
39 H6 H H6 N N N 0 -0.905 1.593 -1.278
40 H7 H H7 N N N 0 -2.426 0.968 1.293
41 H8 H H8 N N N 0 -3.519 2.723 -0.135
42 H9 H H9 N N N 0 -3.486 1.582 -1.502
43 H10 H H10 N N N 0 9.427 1.125 1.085
44 H11 H H11 N N N 0 -4.842 -0.028 -0.191
45 H12 H H12 N N N 0 -4.875 1.113 1.175
46 H13 H H13 N N N 0 6.666 1.8 2.457
47 H14 H H14 N N N 0 -6.014 2.79 -0.252
48 H15 H H15 N N N 0 -5.981 1.65 -1.618
49 H16 H H16 N N N 0 -7.337 0.04 -0.308
50 H17 H H17 N N N 0 -7.37 1.18 1.059
51 H18 H H18 N N N 0 -8.509 2.857 -0.369
52 H19 H H19 N N N 0 -8.476 1.717 -1.735
53 H20 H H20 N N N 0 -9.831 0.107 -0.425
54 H21 H H21 N N N 0 -9.865 1.247 0.942
55 H22 H H22 N N N 0 -11.004 2.924 -0.486
56 H23 H H23 N N N 0 -10.97 1.784 -1.852
57 H24 H H24 N N N 0 -12.326 0.174 -0.542
58 H25 H H25 N N N 0 -12.36 1.314 0.825
59 H26 H H26 N N N 0 -13.168 1.734 -0.705
60 H27 H H27 N N N 0 -0.004 2.194 2.183
61 H28 H H28 N N N 0 -3.381 -2.864 -0.953
62 H29 H H29 N N N 0 -1.917 -3.146 0.019
63 H30 H H30 N N N 0 -3.322 -3.514 2.028
64 H31 H H31 N N N 0 -4.786 -3.231 1.056
65 H32 H H32 N N N 0 -4.197 -5.157 -0.391
66 H33 H H33 N N N 0 -2.733 -5.439 0.581
67 H34 H H34 N N N 0 -5.603 -5.525 1.619
68 H35 H H35 N N N 0 -4.576 -6.941 1.29
69 H36 H H36 N N N 0 -4.139 -5.807 2.591
70 HO3 H H37 N N N 0 4.823 2.322 1.441
71 H1 H H38 N N N 0 2.379 0.747 -2.267
72 H2 H H40 N N N 0 2.348 -0.108 0.664
73 H3 H H41 N N N 0 3.898 2.111 -0.752
74 H4 H H42 N N N 0 4.862 -0.489 0.53
75 H5 H H43 N N N 0 4.778 0.382 -2.396
76 H61 H H44 N N N 0 5.594 -2.265 -1.115
77 H62 H H45 N N N 0 6.735 -1.04 -1.718
78 O1 O O11 N N Y 0 1.066 -0.692 -1.578
79 H39 H H39 N N N 0 0.918 -1.137 -2.424



VJ4 : Chemical Bonds

Total Number of Bonds: 79
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C sing 1.43 N N
2 C6 C5 C C sing 1.53 N N
3 O9 P1 O P doub 1.48 N N
4 C5 O5 C O sing 1.43 N N
5 C5 C4 C C sing 1.53 N N
6 O5 C1 O C sing 1.43 N N
7 O8 P1 O P sing 1.61 N N
8 P1 O4 P O sing 1.61 N N
9 P1 O7 P O sing 1.61 N N
10 O4 C4 O C sing 1.43 N N
11 C4 C3 C C sing 1.53 N N
12 C1 C2 C C sing 1.53 N N
13 C3 C2 C C sing 1.53 N N
14 C3 O3 C O sing 1.43 N N
15 C2 N2 C N sing 1.47 N N
16 N2 C13 N C sing 1.47 N N
17 O2 C13 O C sing 1.43 N N
18 C13 C14 C C sing 1.53 N N
19 O10 C12 O C doub 1.21 N N
20 C12 O11 C O sing 1.34 N N
21 C12 C21 C C sing 1.51 N N
22 C14 C15 C C sing 1.53 N N
23 O11 C15 O C sing 1.45 N N
24 C21 C31 C C sing 1.53 N N
25 C15 C16 C C sing 1.53 N N
26 C16 C17 C C sing 1.53 N N
27 C31 C41 C C sing 1.53 N N
28 C17 C18 C C sing 1.53 N N
29 C18 C7 C C sing 1.53 N N
30 C41 C51 C C sing 1.53 N N
31 C7 C8 C C sing 1.53 N N
32 C8 C9 C C sing 1.53 N N
33 C9 C10 C C sing 1.53 N N
34 C10 C11 C C sing 1.53 N N
35 N2 HN21 N H sing 1.01 N N
36 O6 HO6 O H sing 0.97 N N
37 C13 H37 C H sing 1.09 N N
38 C14 H38 C H sing 1.09 N N
39 C14 H6 C H sing 1.09 N N
40 C15 H7 C H sing 1.09 N N
41 C16 H8 C H sing 1.09 N N
42 C16 H9 C H sing 1.09 N N
43 O7 H10 O H sing 0.97 N N
44 C17 H11 C H sing 1.09 N N
45 C17 H12 C H sing 1.09 N N
46 O8 H13 O H sing 0.97 N N
47 C18 H14 C H sing 1.09 N N
48 C18 H15 C H sing 1.09 N N
49 C7 H16 C H sing 1.09 N N
50 C7 H17 C H sing 1.09 N N
51 C8 H18 C H sing 1.09 N N
52 C8 H19 C H sing 1.09 N N
53 C9 H20 C H sing 1.09 N N
54 C9 H21 C H sing 1.09 N N
55 C10 H22 C H sing 1.09 N N
56 C10 H23 C H sing 1.09 N N
57 C11 H24 C H sing 1.09 N N
58 C11 H25 C H sing 1.09 N N
59 C11 H26 C H sing 1.09 N N
60 O2 H27 O H sing 0.97 N N
61 C21 H28 C H sing 1.09 N N
62 C21 H29 C H sing 1.09 N N
63 C31 H30 C H sing 1.09 N N
64 C31 H31 C H sing 1.09 N N
65 C41 H32 C H sing 1.09 N N
66 C41 H33 C H sing 1.09 N N
67 C51 H34 C H sing 1.09 N N
68 C51 H35 C H sing 1.09 N N
69 C51 H36 C H sing 1.09 N N
70 O3 HO3 O H sing 0.97 N N
71 C1 H1 C H sing 1.09 N N
72 C2 H2 C H sing 1.09 N N
73 C3 H3 C H sing 1.09 N N
74 C4 H4 C H sing 1.09 N N
75 C5 H5 C H sing 1.09 N N
76 C6 H61 C H sing 1.09 N N
77 C6 H62 C H sing 1.09 N N
78 C1 O1 C O sing 1.43 N N
79 O1 H39 O H sing 0.97 N N



VJ4 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VJ4 6xlp Open in New Window s 1 1