Chemical Components in the PDB

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4IX : Summary

Code

4IX

One-letter code

X

Molecule name

(2R,3R,4S,5S,6R)-2-[4-[1-[3-[6-[(Z)-hydroxyiminomethyl]-5-oxidanyl-pyridin-2-yl]propyl]-1,2,3-triazol-4-yl]butoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{R},3~{R},4~{S},5~{S},6~{R})-2-[4-[1-[3-[6-[(~{Z})-hydroxyiminomethyl]-5-oxidanyl-pyridin-2-yl]propyl]-1,2,3-triazol-4-yl]butoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Formula

C21 H31 N5 O8

Formal charge

0

Molecular weight

481.5 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC[CH]1O[CH](OCCCCc2cn(CCCc3ccc(O)c(C=NO)n3)nn2)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.7 c1cc(c(nc1CCCn2cc(nn2)CCCCOC3C(C(C(C(O3)CO)O)O)O)C=NO)O
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@@H](OCCCCc2cn(CCCc3ccc(O)c(\C=N/O)n3)nn2)[C@H](O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(c(nc1CCCn2cc(nn2)CCCCO[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)/C=N\O)O

IUPAC InChI

InChI=1S/C21H31N5O8/c27-12-17-18(29)19(30)20(31)21(34-17)33-9-2-1-4-14-11-26(25-24-14)8-3-5-13-6-7-16(28)15(23-13)10-22-32/h6-7,10-11,17-21,27-32H,1-5,8-9,12H2/b22-10-/t17-,18-,19+,20-,21-/m1/s1

IUPAC InChI key

XSKZXNAZWMWYGQ-WXHIOXNPSA-N
4IX

wwPDB Information

Atom count

65 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-07-02

Last modified at

2021-12-24

Status

Released

Obsoleted

Not Assigned



4IX : Atoms of Molecule

Total Number of Atoms: 65
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C1 N N N 0 8.043 2.648 -0.376
2 C03 C C2 R N N 0 7.894 1.272 0.277
3 C05 C C3 R N N 0 6.47 -0.656 0.344
4 C07 C C4 N N N 0 4.09 -0.452 0.141
5 C08 C C5 N N N 0 2.865 -1.113 -0.494
6 C09 C C6 N N N 0 1.609 -0.32 -0.126
7 C10 C C7 N N N 0 0.385 -0.981 -0.762
8 C11 C C8 N Y N 0 -0.853 -0.201 -0.399
9 C12 C C9 N Y N 0 -1.76 0.323 -1.256
10 C14 C C10 N N N 0 -3.877 1.643 -0.981
11 C15 C C11 N N N 0 -5.131 1.056 -0.329
12 C16 C C12 N N N 0 -6.367 1.797 -0.842
13 C17 C C13 N Y N 0 -7.602 1.219 -0.2
14 C18 C C14 N Y N 0 -8.474 2.056 0.476
15 C19 C C15 N Y N 0 -9.609 1.525 1.066
16 C20 C C16 N Y N 0 -9.834 0.157 0.958
17 C22 C C17 N Y N 0 -8.909 -0.628 0.259
18 C23 C C18 N N N 0 -9.129 -2.082 0.132
19 C29 C C19 R N N 0 7.637 -1.59 0.017
20 C31 C C20 S N N 0 8.936 -0.979 0.554
21 C33 C C21 S N N 0 9.12 0.415 -0.052
22 N13 N N1 N Y N 0 -2.694 0.933 -0.489
23 N24 N N2 N N N 0 -8.277 -2.811 -0.512
24 N26 N N3 N Y N 0 -7.837 -0.072 -0.295
25 N27 N N4 N Y N 0 -2.363 0.783 0.746
26 N28 N N5 N Y N 0 -1.273 0.106 0.834
27 O01 O O1 N N N 0 6.958 3.486 0.026
28 O04 O O2 N N N 0 6.719 0.632 -0.223
29 O06 O O3 N N N 0 5.263 -1.192 -0.203
30 O21 O O4 N N N 0 -10.933 -0.408 1.521
31 O25 O O5 N N N 0 -7.133 -2.215 -1.095
32 O30 O O6 N N N 0 7.418 -2.862 0.631
33 O32 O O7 N N N 0 10.041 -1.809 0.19
34 O34 O O8 N N N 0 10.29 1.024 0.496
35 H021 H H1 N N N 0 8.986 3.098 -0.064
36 H022 H H2 N N N 0 8.035 2.538 -1.461
37 H031 H H3 N N N 0 7.813 1.39 1.357
38 H051 H H4 N N N 0 6.369 -0.563 1.426
39 H072 H H5 N N N 0 4.184 0.57 -0.227
40 H071 H H6 N N N 0 3.974 -0.438 1.225
41 H082 H H7 N N N 0 2.981 -1.127 -1.578
42 H081 H H8 N N N 0 2.772 -2.134 -0.126
43 H091 H H9 N N N 0 1.493 -0.307 0.958
44 H092 H H10 N N N 0 1.703 0.701 -0.494
45 H101 H H11 N N N 0 0.501 -0.995 -1.845
46 H102 H H12 N N N 0 0.291 -2.003 -0.393
47 H121 H H13 N N N 0 -1.742 0.265 -2.334
48 H141 H H14 N N N 0 -3.944 1.531 -2.063
49 H142 H H15 N N N 0 -3.798 2.7 -0.729
50 H152 H H16 N N N 0 -5.21 -0.002 -0.581
51 H151 H H17 N N N 0 -5.064 1.167 0.753
52 H161 H H18 N N N 0 -6.287 2.854 -0.59
53 H162 H H19 N N N 0 -6.434 1.685 -1.924
54 H181 H H20 N N N 0 -8.271 3.115 0.543
55 H191 H H21 N N N 0 -10.303 2.158 1.599
56 H231 H H22 N N N 0 -10.001 -2.537 0.578
57 H291 H H23 N N N 0 7.713 -1.715 -1.063
58 H311 H H24 N N N 0 8.88 -0.902 1.64
59 H331 H H25 N N N 0 9.225 0.331 -1.134
60 H011 H H26 N N N 0 6.988 4.376 -0.352
61 H211 H H27 N N N 0 -11.702 -0.439 0.936
62 H251 H H28 N N N 0 -6.555 -2.839 -1.556
63 H301 H H29 N N N 0 6.609 -3.305 0.34
64 H321 H H30 N N N 0 9.986 -2.71 0.535
65 H341 H H31 N N N 0 11.106 0.534 0.326



4IX : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O01 C02 O C sing 1.43 N N
2 C02 C03 C C sing 1.53 N N
3 O34 C33 O C sing 1.43 N N
4 O30 C29 O C sing 1.43 N N
5 C03 C33 C C sing 1.53 N N
6 C03 O04 C O sing 1.43 N N
7 C33 C31 C C sing 1.53 N N
8 O04 C05 O C sing 1.43 N N
9 C31 C29 C C sing 1.53 N N
10 C31 O32 C O sing 1.43 N N
11 C29 C05 C C sing 1.53 N N
12 C05 O06 C O sing 1.43 N N
13 O06 C07 O C sing 1.43 N N
14 C07 C08 C C sing 1.53 N N
15 C08 C09 C C sing 1.53 N N
16 N28 N27 N N doub 1.29 N Y
17 N28 C11 N C sing 1.34 N Y
18 N27 N13 N N sing 1.29 N Y
19 C09 C10 C C sing 1.53 N N
20 C11 C10 C C sing 1.51 N N
21 C11 C12 C C doub 1.35 N Y
22 N13 C14 N C sing 1.46 N N
23 N13 C12 N C sing 1.35 N Y
24 C14 C15 C C sing 1.53 N N
25 C18 C19 C C doub 1.39 N Y
26 C18 C17 C C sing 1.38 N Y
27 C19 C20 C C sing 1.39 N Y
28 C15 C16 C C sing 1.53 N N
29 C16 C17 C C sing 1.51 N N
30 C17 N26 C N doub 1.32 N Y
31 C20 O21 C O sing 1.36 N N
32 C20 C22 C C doub 1.4 N Y
33 N26 C22 N C sing 1.33 N Y
34 C22 C23 C C sing 1.48 N N
35 C23 N24 C N doub 1.29 Z N
36 O25 N24 O N sing 1.42 N N
37 C02 H021 C H sing 1.09 N N
38 C02 H022 C H sing 1.09 N N
39 C03 H031 C H sing 1.09 N N
40 C05 H051 C H sing 1.09 N N
41 C07 H072 C H sing 1.09 N N
42 C07 H071 C H sing 1.09 N N
43 C08 H082 C H sing 1.09 N N
44 C08 H081 C H sing 1.09 N N
45 C09 H091 C H sing 1.09 N N
46 C09 H092 C H sing 1.09 N N
47 C10 H101 C H sing 1.09 N N
48 C10 H102 C H sing 1.09 N N
49 C12 H121 C H sing 1.08 N N
50 C14 H141 C H sing 1.09 N N
51 C14 H142 C H sing 1.09 N N
52 C15 H152 C H sing 1.09 N N
53 C15 H151 C H sing 1.09 N N
54 C16 H161 C H sing 1.09 N N
55 C16 H162 C H sing 1.09 N N
56 C18 H181 C H sing 1.08 N N
57 C19 H191 C H sing 1.08 N N
58 C23 H231 C H sing 1.08 N N
59 C29 H291 C H sing 1.09 N N
60 C31 H311 C H sing 1.09 N N
61 C33 H331 C H sing 1.09 N N
62 O01 H011 O H sing 0.97 N N
63 O21 H211 O H sing 0.97 N N
64 O25 H251 O H sing 0.97 N N
65 O30 H301 O H sing 0.97 N N
66 O32 H321 O H sing 0.97 N N
67 O34 H341 O H sing 0.97 N N



4IX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
4IX 7p1p Open in New Window Bound ligand 1 1