Chemical Components in the PDB

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O34 : Summary

Code

O34

One-letter code

X

Molecule name

yersiniabactin

Systematic names

ProgramVersionName
ACDLabs 12.01 (4S)-2-[(1S)-1-hydroxy-1-{(2R,4R)-2-[(4R)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-1,3-thiazolidin-4-yl}-2-methylpropan-2-yl]-4-methyl-4,5-dihydro-1,3-thiazole-4-carboxylic acid
OpenEye OEToolkits 2.0.7 (4~{S})-2-[(1~{S})-1-[(2~{R},4~{R})-2-[(4~{R})-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-1,3-thiazolidin-4-yl]-2-methyl-1-oxidanyl-propan-2-yl]-4-methyl-5~{H}-1,3-thiazole-4-carboxylic acid

Formula

C21 H27 N3 O4 S3

Formal charge

0

Molecular weight

481.652 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N1=C(SCC1C2NC(CS2)C(O)C(C3=NC(CS3)(C(O)=O)C)(C)C)c4c(O)cccc4
SMILES CACTVS 3.385 CC(C)([CH](O)[CH]1CS[CH](N1)[CH]2CSC(=N2)c3ccccc3O)C4=N[C](C)(CS4)C(O)=O
SMILES OpenEye OEToolkits 2.0.7 CC1(CSC(=N1)C(C)(C)C(C2CSC(N2)C3CSC(=N3)c4ccccc4O)O)C(=O)O
Canonical SMILES CACTVS 3.385 CC(C)([C@H](O)[C@@H]1CS[C@@H](N1)[C@H]2CSC(=N2)c3ccccc3O)C4=N[C@](C)(CS4)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@]1(CSC(=N1)C(C)(C)[C@@H]([C@@H]2CS[C@@H](N2)[C@H]3CSC(=N3)c4ccccc4O)O)C(=O)O

IUPAC InChI

InChI=1S/C21H27N3O4S3/c1-20(2,18-24-21(3,10-31-18)19(27)28)15(26)12-8-30-17(22-12)13-9-29-16(23-13)11-6-4-5-7-14(11)25/h4-7,12-13,15,17,22,25-26H,8-10H2,1-3H3,(H,27,28)/t12-,13+,15+,17+,21+/m0/s1

IUPAC InChI key

JHYVWAMMAMCUIR-NIJJZIDKSA-N
O34

wwPDB Information

Atom count

58 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-06-05

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



O34 : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -2.416 0.35 -0.087
2 N2 N N2 N N N 0 -0.155 -0.912 -1.253
3 N3 N N3 N N N 0 2.601 0.23 0.822
4 O1 O O1 N N N 0 -3.349 -1.751 1.16
5 O2 O O2 N N N 0 3.044 -2.697 -1.803
6 O3 O O3 N N N 0 2.726 1.762 3.132
7 O4 O O4 N N N 0 4.886 1.99 2.727
8 S1 S S1 N N N 0 -3.729 2.327 -0.919
9 S2 S S2 N N N 0 0.796 1.26 -2.391
10 S3 S S3 N N N 0 4.59 -0.97 -0.125
11 C1 C C1 N Y N 0 -4.594 -1.217 1.074
12 C2 C C2 N Y N 0 -5.68 -1.896 1.606
13 C3 C C3 N Y N 0 -6.947 -1.352 1.518
14 C4 C C4 N Y N 0 -7.141 -0.127 0.9
15 C5 C C5 N Y N 0 -6.071 0.56 0.367
16 C6 C C6 N Y N 0 -4.786 0.023 0.454
17 C7 C C7 N N N 0 -3.634 0.758 -0.111
18 C8 C C8 N N N 0 -1.945 2.458 -1.267
19 C9 C C9 R N N 0 -1.373 1.161 -0.675
20 C10 C C10 R N N 0 -0.685 0.364 -1.785
21 C11 C C11 N N N 0 2.004 -0.075 -2.024
22 C12 C C12 R N N 0 1.069 -1.314 -1.972
23 C13 C C13 S N N 0 1.76 -2.457 -1.224
24 C14 C C14 N N N 0 1.927 -2.075 0.248
25 C15 C C15 N N N 0 0.571 -1.664 0.825
26 C19 C C19 S N N 0 3.612 1.262 0.883
27 C16 C C16 N N N 0 2.471 -3.274 1.027
28 C17 C C17 N N N 0 2.891 -0.922 0.361
29 C18 C C18 N N N 0 4.958 0.752 0.342
30 C20 C C20 N N N 0 3.157 2.461 0.048
31 C21 C C21 N N N 0 3.788 1.698 2.315
32 H1 H H1 N N N 0 -0.854 -1.639 -1.294
33 H8 H H8 N N N 0 -5.536 -2.851 2.089
34 H5 H H5 N N N 0 -3.11 -2.315 0.412
35 H6 H H6 N N N 0 3.638 -1.934 -1.772
36 H7 H H7 N N N 0 2.888 2.047 4.042
37 H9 H H9 N N N 0 -7.79 -1.884 1.932
38 H10 H H10 N N N 0 -8.135 0.291 0.836
39 H11 H H11 N N N 0 -6.227 1.514 -0.114
40 H12 H H12 N N N 0 -1.765 2.503 -2.341
41 H13 H H13 N N N 0 -1.52 3.331 -0.77
42 H14 H H14 N N N 0 -0.64 1.41 0.091
43 H15 H H15 N N N 0 -1.377 0.176 -2.606
44 H16 H H16 N N N 0 2.739 -0.17 -2.824
45 H17 H H17 N N N 0 2.492 0.09 -1.063
46 H18 H H18 N N N 0 0.817 -1.631 -2.984
47 H19 H H19 N N N 0 1.153 -3.359 -1.299
48 H20 H H20 N N N 0 -0.203 -2.331 0.445
49 H21 H H21 N N N 0 0.604 -1.729 1.913
50 H22 H H22 N N N 0 0.345 -0.64 0.529
51 H23 H H23 N N N 0 3.437 -3.566 0.615
52 H24 H H24 N N N 0 2.59 -3.002 2.076
53 H25 H H25 N N N 0 1.774 -4.107 0.945
54 H27 H H27 N N N 0 5.722 0.786 1.118
55 H28 H H28 N N N 0 5.266 1.33 -0.529
56 H29 H H29 N N N 0 2.231 2.861 0.461
57 H30 H H30 N N N 0 3.927 3.232 0.07
58 H31 H H31 N N N 0 2.988 2.144 -0.981



O34 : Chemical Bonds

Total Number of Bonds: 61
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C15 C14 C C sing 1.53 N N
2 S2 C11 S C sing 1.84 N N
3 S2 C10 S C sing 1.83 N N
4 C11 C12 C C sing 1.55 N N
5 C12 N2 C N sing 1.48 N N
6 C12 C13 C C sing 1.53 N N
7 S3 C17 S C sing 1.77 N N
8 S3 C18 S C sing 1.82 N N
9 C14 C13 C C sing 1.53 N N
10 C14 C17 C C sing 1.51 N N
11 C14 C16 C C sing 1.53 N N
12 C10 N2 C N sing 1.48 N N
13 C10 C9 C C sing 1.53 N N
14 C13 O2 C O sing 1.43 N N
15 C17 N3 C N doub 1.27 N N
16 C18 C19 C C sing 1.54 N N
17 N3 C19 N C sing 1.45 N N
18 C9 C8 C C sing 1.54 N N
19 C9 N1 C N sing 1.45 N N
20 C19 C21 C C sing 1.51 N N
21 C19 C20 C C sing 1.53 N N
22 C8 S1 C S sing 1.82 N N
23 C21 O4 C O doub 1.21 N N
24 C21 O3 C O sing 1.34 N N
25 N1 C7 N C doub 1.28 N N
26 S1 C7 S C sing 1.77 N N
27 C7 C6 C C sing 1.48 N N
28 O1 C1 O C sing 1.36 N N
29 C6 C1 C C doub 1.4 N Y
30 C6 C5 C C sing 1.4 N Y
31 C1 C2 C C sing 1.39 N Y
32 C5 C4 C C doub 1.38 N Y
33 C2 C3 C C doub 1.38 N Y
34 C4 C3 C C sing 1.39 N Y
35 N2 H1 N H sing 1.01 N N
36 O1 H5 O H sing 0.97 N N
37 O2 H6 O H sing 0.97 N N
38 O3 H7 O H sing 0.97 N N
39 C2 H8 C H sing 1.08 N N
40 C3 H9 C H sing 1.08 N N
41 C4 H10 C H sing 1.08 N N
42 C5 H11 C H sing 1.08 N N
43 C8 H12 C H sing 1.09 N N
44 C8 H13 C H sing 1.09 N N
45 C9 H14 C H sing 1.09 N N
46 C10 H15 C H sing 1.09 N N
47 C11 H16 C H sing 1.09 N N
48 C11 H17 C H sing 1.09 N N
49 C12 H18 C H sing 1.09 N N
50 C13 H19 C H sing 1.09 N N
51 C15 H20 C H sing 1.09 N N
52 C15 H21 C H sing 1.09 N N
53 C15 H22 C H sing 1.09 N N
54 C16 H23 C H sing 1.09 N N
55 C16 H24 C H sing 1.09 N N
56 C16 H25 C H sing 1.09 N N
57 C18 H27 C H sing 1.09 N N
58 C18 H28 C H sing 1.09 N N
59 C20 H29 C H sing 1.09 N N
60 C20 H30 C H sing 1.09 N N
61 C20 H31 C H sing 1.09 N N



O34 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
O34 6p6j Open in New Window Bound ligand 1 1