Chemical Components in the PDB

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Y3U : Summary

Code

Y3U

One-letter code

X

Molecule name

[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate

Formula

C19 H24 N4 O10 S

Formal charge

0

Molecular weight

500.48 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1C(=O)C=CN([CH]2O[CH](CO[S](=O)(=O)NC(=O)[CH](N)Cc3ccc(O)cc3)[CH](O)[CH]2O)C1=O
SMILES OpenEye OEToolkits 2.0.6 CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(Cc3ccc(cc3)O)N)O)O
Canonical SMILES CACTVS 3.385 CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)Cc3ccc(O)cc3)[C@@H](O)[C@H]2O)C1=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](Cc3ccc(cc3)O)N)O)O

IUPAC InChI

InChI=1S/C19H24N4O10S/c1-22-14(25)6-7-23(19(22)29)18-16(27)15(26)13(33-18)9-32-34(30,31)21-17(28)12(20)8-10-2-4-11(24)5-3-10/h2-7,12-13,15-16,18,24,26-27H,8-9,20H2,1H3,(H,21,28)/t12-,13+,15+,16+,18+/m0/s1

IUPAC InChI key

JZICRHJSYJTEMP-IQNGCQKYSA-N
Y3U

wwPDB Information

Atom count

58 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-08-10

Last modified at

2019-04-12

Status

Released

Obsoleted

Not Assigned



Y3U : 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 C3U C C1 N N N 0 5.254 -4.095 1.589
2 N3 N N1 N N N 0 4.331 -3.331 0.746
3 C4 C C2 N N N 0 3.387 -3.974 0.029
4 O4 O O1 N N N 0 3.299 -5.188 0.079
5 C5 C C3 N N N 0 2.5 -3.226 -0.781
6 C6 C C4 N N N 0 2.62 -1.881 -0.818
7 N1 N N2 N N N 0 3.591 -1.266 -0.076
8 C1' C C5 R N N 0 3.72 0.192 -0.116
9 O4' O O2 N N N 0 2.456 0.818 0.192
10 C4' C C6 R N N 0 2.552 2.155 -0.345
11 C5' C C7 N N N 0 1.157 2.748 -0.551
12 O5' O O3 N N N 0 0.528 2.937 0.718
13 SBI S S1 N N N 0 -0.873 3.526 0.633
14 OAD O O4 N N N 0 -1.262 3.831 1.966
15 OAE O O5 N N N 0 -0.84 4.493 -0.407
16 NAT N N3 N N N 0 -1.882 2.318 0.117
17 C C C8 N N N 0 -2.089 1.235 0.892
18 O O O6 N N N 0 -1.536 1.145 1.968
19 CA C C9 S N N 0 -3.006 0.136 0.422
20 N N N4 N N N 0 -2.711 -1.098 1.162
21 CB C C10 N N N 0 -4.46 0.544 0.671
22 CG C C11 N Y N 0 -5.381 -0.498 0.091
23 CD1 C C12 N Y N 0 -5.81 -0.387 -1.219
24 CE1 C C13 N Y N 0 -6.654 -1.342 -1.753
25 CZ C C14 N Y N 0 -7.07 -2.412 -0.974
26 OH O O7 N N N 0 -7.9 -3.352 -1.498
27 CE2 C C15 N Y N 0 -6.638 -2.52 0.339
28 CD2 C C16 N Y N 0 -5.79 -1.566 0.867
29 C3' C C17 S N N 0 3.269 1.985 -1.703
30 O3' O O8 N N N 0 4.161 3.076 -1.939
31 C2' C C18 R N N 0 4.056 0.663 -1.548
32 O2' O O9 N N N 0 5.459 0.897 -1.683
33 C2 C C19 N N N 0 4.425 -1.989 0.694
34 O2 O O10 N N N 0 5.278 -1.422 1.349
35 H1 H H1 N N N 0 4.827 -4.208 2.585
36 H2 H H2 N N N 0 5.418 -5.078 1.149
37 H3 H H3 N N N 0 6.205 -3.565 1.658
38 H4 H H4 N N N 0 1.738 -3.723 -1.362
39 H5 H H5 N N N 0 1.952 -1.294 -1.431
40 H6 H H6 N N N 0 4.488 0.524 0.584
41 H7 H H7 N N N 0 3.141 2.789 0.318
42 H8 H H8 N N N 0 1.241 3.708 -1.061
43 H9 H H9 N N N 0 0.558 2.067 -1.155
44 H10 H H10 N N N 0 -2.324 2.39 -0.743
45 H11 H H11 N N N 0 -2.854 -0.033 -0.643
46 H12 H H12 N N N 0 -1.777 -1.424 0.964
47 H13 H H13 N N N 0 -2.845 -0.966 2.153
48 H15 H H15 N N N 0 -4.635 0.628 1.743
49 H16 H H16 N N N 0 -4.654 1.506 0.195
50 H17 H H17 N N N 0 -5.486 0.446 -1.825
51 H18 H H18 N N N 0 -6.99 -1.255 -2.776
52 H19 H H19 N N N 0 -7.441 -4.092 -1.918
53 H20 H H20 N N N 0 -6.961 -3.352 0.947
54 H21 H H21 N N N 0 -5.45 -1.653 1.888
55 H22 H H22 N N N 0 2.543 1.904 -2.511
56 H23 H H23 N N N 0 4.638 3.02 -2.778
57 H24 H H24 N N N 0 3.718 -0.07 -2.281
58 H25 H H25 N N N 0 5.725 1.196 -2.564



Y3U : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3U N3 C N sing 1.47 N N
2 O2 C2 O C doub 1.22 N N
3 N3 C2 N C sing 1.35 N N
4 N3 C4 N C sing 1.35 N N
5 C2 N1 C N sing 1.35 N N
6 O4 C4 O C doub 1.22 N N
7 C4 C5 C C sing 1.42 N N
8 N1 C1' N C sing 1.46 N N
9 N1 C6 N C sing 1.37 N N
10 C1' O4' C O sing 1.44 N N
11 C1' C2' C C sing 1.54 N N
12 O4' C4' O C sing 1.44 N N
13 C5 C6 C C doub 1.35 N N
14 O3' C3' O C sing 1.43 N N
15 C4' C3' C C sing 1.55 N N
16 C4' C5' C C sing 1.53 N N
17 O2' C2' O C sing 1.43 N N
18 C2' C3' C C sing 1.55 N N
19 C5' O5' C O sing 1.43 N N
20 O5' SBI O S sing 1.52 N N
21 CE1 CD1 C C doub 1.38 N Y
22 CE1 CZ C C sing 1.39 N Y
23 CD1 CG C C sing 1.38 N Y
24 SBI NAT S N sing 1.66 N N
25 SBI OAE S O doub 1.42 N N
26 SBI OAD S O doub 1.42 N N
27 NAT C N C sing 1.35 N N
28 OH CZ O C sing 1.36 N N
29 CZ CE2 C C doub 1.39 N Y
30 CG CB C C sing 1.51 N N
31 CG CD2 C C doub 1.38 N Y
32 CB CA C C sing 1.53 N N
33 CA C C C sing 1.51 N N
34 CA N C N sing 1.47 N N
35 C O C O doub 1.21 N N
36 CE2 CD2 C C sing 1.38 N Y
37 C3U H1 C H sing 1.09 N N
38 C3U H2 C H sing 1.09 N N
39 C3U H3 C H sing 1.09 N N
40 C5 H4 C H sing 1.08 N N
41 C6 H5 C H sing 1.08 N N
42 C1' H6 C H sing 1.09 N N
43 C4' H7 C H sing 1.09 N N
44 C5' H8 C H sing 1.09 N N
45 C5' H9 C H sing 1.09 N N
46 NAT H10 N H sing 0.97 N N
47 CA H11 C H sing 1.09 N N
48 N H12 N H sing 1.01 N N
49 N H13 N H sing 1.01 N N
50 CB H15 C H sing 1.09 N N
51 CB H16 C H sing 1.09 N N
52 CD1 H17 C H sing 1.08 N N
53 CE1 H18 C H sing 1.08 N N
54 OH H19 O H sing 0.97 N N
55 CE2 H20 C H sing 1.08 N N
56 CD2 H21 C H sing 1.08 N N
57 C3' H22 C H sing 1.09 N N
58 O3' H23 O H sing 0.97 N N
59 C2' H24 C H sing 1.09 N N
60 O2' H25 O H sing 0.97 N N



Y3U : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Y3U 6hb7 Open in New Window Bound ligand 2 1